from k1lib.imports import *
Explores the cif file type more. Pretty much just prints out column frequencies of all tables. Remember to read this together with the last notebook, to serve as a reference.
hasTable = filt(grep("loop_") | shape(0) | (op() > 0))
preprocess = ~head(2) | ((filt(op().startswith("_")) | op().split(".")[1].all()) & (~filt(op().startswith("_")) | aS(k1a.str_split, " ").all()))\
| ~aS(lambda x, y: [x | insertIdColumn() | ~apply(lambda x, y: f"{x} {y}"), *y])
freqs = transpose() | (head(1) & (~head(1) | count() | ~sort() | head(6)) | joinStreams()).all()
cuts = lambda *c: (cut(*c) & ~cut(*c))
blocks = "../1-spike-protein/6VXX.cif" | cat() | grep("^#", sep=True).till() | deref() | aS(k1.Wrapper)
_tables = blocks() | hasTable | preprocess.all() | deref() | aS(k1.Wrapper) # list of blocks that are tables
def tables(i=None):
if i is None: return _tables()
print("-"*20, blocks() | hasTable | rows(i) | item() | rows(2) | item() | op().split(".")[0], "-"*20)
return _tables() | rows(i) | item()
blocks() | shape(), blocks() | hasTable | shape()
((74, 2, 1), (36, 7, 1))
tables(0) | display()
-------------------- _database_2 -------------------- 0 database_id 1 database_code pdb 6VXX wwpdb D_1000247293 emdb EMD-21452
tables(1) | display()
-------------------- _pdbx_database_related -------------------- 0 db_name 1 details 2 db_id 3 content_type EMDB 'Structure of the SARS-CoV-2 spike glycoprotein (closed state)' EMD-21452 'associated EM volume' EMDB 'Structure of the SARS-CoV-2 spike glycoprotein (open state)' EMD-21457 'other EM volume'
tables(2) | display(None)
-------------------- _audit_author -------------------- 0 name 1 pdbx_ordinal 2 identifier_ORCID 'Walls, A.C.' 1 ? 'Park, Y.J.' 2 ? 'Tortorici, M.A.' 3 ? 'Wall, A.' 4 ? 'Seattle Structural Genomics Center for Infectious Disease (SSGCID)' 5 ? 'McGuire, A.T.' 6 ? 'Veesler, D.' 7 ?
tables(3) | display(None)
-------------------- _citation_author -------------------- 0 citation_id 1 name 2 ordinal primary 'Walls, A.C.' 1 primary 'Park, Y.J.' 2 primary 'Tortorici, M.A.' 3 primary 'Wall, A.' 4 primary 'McGuire, A.T.' 5 primary 'Veesler, D.' 6
tables(4) | display()
-------------------- _entity -------------------- 0 details 1 formula_weight 2 id 3 src_method 4 type 5 pdbx_description 6 pdbx_number_of_molecules 7 pdbx_mutation 8 pdbx_fragment 9 pdbx_ec ? 141532.797 1 man polymer 'Spike glycoprotein' 3 ? ectodomain ? ? 424.401 2 man branched 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose 15 ? ? ? ? 221.208 3 man non-polymer 2-acetamido-2-deoxy-beta-D-glucopyranose 33 ? ? ?
tables(5) | (display() & shape()) | deref()
-------------------- _entity_poly_seq -------------------- 0 entity_id 1 hetero 2 mon_id 3 num 1 n MET 1 1 n GLY 2 1 n ILE 3 1 n LEU 4 1 n PRO 5 1 n SER 6 1 n PRO 7 1 n GLY 8 1 n MET 9
[None, [1282, 4, 11]]
tables(5) | freqs | deref()
-------------------- _entity_poly_seq --------------------
[['0 entity_id', [1281, '1', '100%']], ['1 hetero', [1281, 'n', '100%']], ['2 mon_id', [110, 'LEU', '9%'], [100, 'SER', '8%'], [97, 'THR', '8%'], [94, 'VAL', '7%'], [93, 'GLY', '7%'], [89, 'ASN', '7%']], ['3 num', [1, '1', '0%'], [1, '2', '0%'], [1, '3', '0%'], [1, '4', '0%'], [1, '5', '0%'], [1, '6', '0%']]]
tables(6) | display()
-------------------- _struct_ref_seq -------------------- 0 align_id 1 ref_id 2 pdbx_PDB_id_code 3 pdbx_strand_id 4 seq_align_beg 5 pdbx_seq_align_beg_ins_code 6 seq_align_end 7 pdbx_seq_align_end_ins_code 8 pdbx_db_accession 9 db_align_beg 10 pdbx_db_align_beg_ins_code 11 db_align_end 12 pdbx_db_align_end_ins_code 13 pdbx_auth_seq_align_beg 14 pdbx_auth_seq_align_end 1 1 6VXX A 33 . 1230 . P0DTC2 14 . 1211 . 14 1211 2 1 6VXX B 33 . 1230 . P0DTC2 14 . 1211 . 14 1211 3 1 6VXX C 33 . 1230 . P0DTC2 14 . 1211 . 14 1211
tables(7) | (display() & shape()) | deref()
-------------------- _struct_ref_seq_dif -------------------- 0 align_id 1 pdbx_pdb_id_code 2 mon_id 3 pdbx_pdb_strand_id 4 seq_num 5 pdbx_pdb_ins_code 6 pdbx_seq_db_name 7 pdbx_seq_db_accession_code 8 db_mon_id 9 pdbx_seq_db_seq_num 10 details 11 pdbx_auth_seq_num 12 pdbx_ordinal 1 6VXX MET A 1 . UNP P0DTC2 . . 'expression tag' -18 1 1 6VXX GLY A 2 . UNP P0DTC2 . . 'expression tag' -17 2 1 6VXX ILE A 3 . UNP P0DTC2 . . 'expression tag' -16 3 1 6VXX LEU A 4 . UNP P0DTC2 . . 'expression tag' -15 4 1 6VXX PRO A 5 . UNP P0DTC2 . . 'expression tag' -14 5 1 6VXX SER A 6 . UNP P0DTC2 . . 'expression tag' -13 6 1 6VXX PRO A 7 . UNP P0DTC2 . . 'expression tag' -12 7 1 6VXX GLY A 8 . UNP P0DTC2 . . 'expression tag' -11 8 1 6VXX MET A 9 . UNP P0DTC2 . . 'expression tag' -10 9
[None, [265, 13, 10]]
tables(7) | cuts(0, 1, 2, 3, 5, 6, 7, 8, 9, 10) | freqs.all() | deref()
-------------------- _struct_ref_seq_dif --------------------
[[['0 align_id', [88, '1', '33%'], [88, '2', '33%'], [88, '3', '33%']], ['1 pdbx_pdb_id_code', [264, '6VXX', '100%']], ['2 mon_id', [48, 'GLY', '18%'], [36, 'LEU', '14%'], [24, 'SER', '9%'], [24, 'HIS', '9%'], [21, 'PRO', '8%'], [15, 'VAL', '6%']], ['3 pdbx_pdb_strand_id', [88, 'A', '33%'], [88, 'B', '33%'], [88, 'C', '33%']], ['5 pdbx_pdb_ins_code', [264, '.', '100%']], ['6 pdbx_seq_db_name', [264, 'UNP', '100%']], ['7 pdbx_seq_db_accession_code', [264, 'P0DTC2', '100%']], ['8 db_mon_id', [249, '.', '94%'], [9, 'ARG', '3%'], [3, 'LYS', '1%'], [3, 'VAL', '1%']], ['9 pdbx_seq_db_seq_num', [249, '.', '94%'], [3, '682', '1%'], [3, '683', '1%'], [3, '685', '1%'], [3, '986', '1%'], [3, '987', '1%']], ['10 details', [249, "'expression tag'", '94%'], [15, 'conflict', '6%']]], [['4 seq_num', [3, '1', '1%'], [3, '2', '1%'], [3, '3', '1%'], [3, '4', '1%'], [3, '5', '1%'], [3, '6', '1%']], ['11 pdbx_auth_seq_num', [3, '-18', '1%'], [3, '-17', '1%'], [3, '-16', '1%'], [3, '-15', '1%'], [3, '-14', '1%'], [3, '-13', '1%']], ['12 pdbx_ordinal', [1, '1', '0%'], [1, '2', '0%'], [1, '3', '0%'], [1, '4', '0%'], [1, '5', '0%'], [1, '6', '0%']]]]
tables(8) | (display(None) & shape()) | deref()
-------------------- _chem_comp -------------------- 0 formula 1 formula_weight 2 id 3 mon_nstd_flag 4 name 5 type 6 pdbx_synonyms 'C3 H7 N O2' 89.093 ALA y ALANINE 'l-peptide linking' ? 'C6 H15 N4 O2 1' 175.209 ARG y ARGININE 'l-peptide linking' ? 'C4 H8 N2 O3' 132.118 ASN y ASPARAGINE 'l-peptide linking' ? 'C4 H7 N O4' 133.103 ASP y 'ASPARTIC ACID' 'l-peptide linking' ? 'C3 H7 N O2 S' 121.158 CYS y CYSTEINE 'l-peptide linking' ? 'C5 H10 N2 O3' 146.144 GLN y GLUTAMINE 'l-peptide linking' ? 'C5 H9 N O4' 147.129 GLU y 'GLUTAMIC ACID' 'l-peptide linking' ? 'C2 H5 N O2' 75.067 GLY y GLYCINE 'peptide linking' ? 'C6 H10 N3 O2 1' 156.162 HIS y HISTIDINE 'l-peptide linking' ? 'C6 H13 N O2' 131.173 ILE y ISOLEUCINE 'l-peptide linking' ? 'C6 H13 N O2' 131.173 LEU y LEUCINE 'l-peptide linking' ? 'C6 H15 N2 O2 1' 147.195 LYS y LYSINE 'l-peptide linking' ? 'C5 H11 N O2 S' 149.211 MET y METHIONINE 'l-peptide linking' ? 'C8 H15 N O6' 221.208 NAG . 2-acetamido-2-deoxy-beta-D-glucopyranose 'd-saccharide, beta linking' N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE 'C9 H11 N O2' 165.189 PHE y PHENYLALANINE 'l-peptide linking' ? 'C5 H9 N O2' 115.13 PRO y PROLINE 'l-peptide linking' ? 'C3 H7 N O3' 105.093 SER y SERINE 'l-peptide linking' ? 'C4 H9 N O3' 119.119 THR y THREONINE 'l-peptide linking' ? 'C11 H12 N2 O2' 204.225 TRP y TRYPTOPHAN 'l-peptide linking' ? 'C9 H11 N O3' 181.189 TYR y TYROSINE 'l-peptide linking' ? 'C5 H11 N O2' 117.146 VAL y VALINE 'l-peptide linking' ?
[None, [22, 7, 9]]
tables(9) | (display() & shape()) | deref()
-------------------- _struct_asym -------------------- 0 details 1 entity_id 2 id 3 pdbx_modified 4 pdbx_blank_PDB_chainid_flag ? 1 A N N ? 1 B N N ? 1 C N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N ? 2 I N N
[None, [52, 5, 9]]
tables(9) | cuts(0, 1, 3, 4) | freqs.all() | deref()
-------------------- _struct_asym --------------------
[[['0 details', [51, '?', '100%']], ['1 entity_id', [33, '3', '65%'], [15, '2', '29%'], [3, '1', '6%']], ['3 pdbx_modified', [51, 'N', '100%']], ['4 pdbx_blank_PDB_chainid_flag', [51, 'N', '100%']]], [['2 id', [1, 'A', '2%'], [1, 'B', '2%'], [1, 'C', '2%'], [1, 'D', '2%'], [1, 'E', '2%'], [1, 'F', '2%']]]]
tables(10) | (display() & shape()) | deref()
-------------------- _struct_conf -------------------- 0 conf_type_id 1 id 2 beg_label_comp_id 3 beg_label_seq_id 4 pdbx_beg_PDB_ins_code 5 beg_label_asym_id 6 beg_label_entity_id 7 beg_auth_comp_id 8 beg_auth_seq_id 9 beg_auth_asym_id 10 end_label_comp_id 11 end_label_seq_id 12 pdbx_end_PDB_ins_code 13 end_label_asym_id 14 end_label_entity_id 15 end_auth_comp_id 16 end_auth_seq_id 17 end_auth_asym_id 18 pdbx_PDB_helix_class 19 details 20 pdbx_PDB_helix_length helx_p helx_p1 ASP 313 . A 1 ASP 294 A LEU 322 . A 1 LEU 303 A 1 ? 10 helx_p helx_p2 PHE 357 . A 1 PHE 338 A ASN 362 . A 1 ASN 343 A 1 ? 6 helx_p helx_p3 SER 368 . A 1 SER 349 A TRP 372 . A 1 TRP 353 A 5 ? 5 helx_p helx_p4 ASP 383 . A 1 ASP 364 A SER 390 . A 1 SER 371 A 1 ? 8 helx_p helx_p5 ASP 424 . A 1 ASP 405 A ILE 429 . A 1 ILE 410 A 5 ? 6 helx_p helx_p6 ASP 756 . A 1 ASP 737 A CYS 762 . A 1 CYS 743 A 1 ? 7 helx_p helx_p7 SER 765 . A 1 SER 746 A LEU 773 . A 1 LEU 754 A 1 ? 9 helx_p helx_p8 GLN 774 . A 1 GLN 755 A PHE 778 . A 1 PHE 759 A 5 ? 5 helx_p helx_p9 CYS 779 . A 1 CYS 760 A ALA 802 . A 1 ALA 783 A 1 ? 24
[None, [61, 21, 14]]
tables(10) | cuts(0, 2, 4, 5, 6, 7, 9, 10, 12, 13, 14, 15, 17, 18) | freqs.all() | deref()
-------------------- _struct_conf --------------------
[[['0 conf_type_id', [60, 'helx_p', '100%']], ['2 beg_label_comp_id', [15, 'ASP', '25%'], [9, 'SER', '15%'], [6, 'GLN', '10%'], [6, 'LEU', '10%'], [3, 'PHE', '5%'], [3, 'CYS', '5%']], ['4 pdbx_beg_PDB_ins_code', [60, '.', '100%']], ['5 beg_label_asym_id', [20, 'A', '33%'], [20, 'B', '33%'], [20, 'C', '33%']], ['6 beg_label_entity_id', [60, '1', '100%']], ['7 beg_auth_comp_id', [15, 'ASP', '25%'], [9, 'SER', '15%'], [6, 'GLN', '10%'], [6, 'LEU', '10%'], [3, 'PHE', '5%'], [3, 'CYS', '5%']], ['9 beg_auth_asym_id', [20, 'A', '33%'], [20, 'B', '33%'], [20, 'C', '33%']], ['10 end_label_comp_id', [9, 'SER', '15%'], [9, 'GLY', '15%'], [6, 'LEU', '10%'], [6, 'ASN', '10%'], [6, 'ALA', '10%'], [3, 'TRP', '5%']], ['12 pdbx_end_PDB_ins_code', [60, '.', '100%']], ['13 end_label_asym_id', [20, 'A', '33%'], [20, 'B', '33%'], [20, 'C', '33%']], ['14 end_label_entity_id', [60, '1', '100%']], ['15 end_auth_comp_id', [9, 'SER', '15%'], [9, 'GLY', '15%'], [6, 'LEU', '10%'], [6, 'ASN', '10%'], [6, 'ALA', '10%'], [3, 'TRP', '5%']], ['17 end_auth_asym_id', [20, 'A', '33%'], [20, 'B', '33%'], [20, 'C', '33%']], ['18 pdbx_PDB_helix_class', [45, '1', '75%'], [15, '5', '25%']]], [['1 id', [1, 'helx_p1', '2%'], [1, 'helx_p2', '2%'], [1, 'helx_p3', '2%'], [1, 'helx_p4', '2%'], [1, 'helx_p5', '2%'], [1, 'helx_p6', '2%']], ['3 beg_label_seq_id', [3, '313', '5%'], [3, '357', '5%'], [3, '368', '5%'], [3, '383', '5%'], [3, '424', '5%'], [3, '756', '5%']], ['8 beg_auth_seq_id', [3, '294', '5%'], [3, '338', '5%'], [3, '349', '5%'], [3, '364', '5%'], [3, '405', '5%'], [3, '737', '5%']], ['11 end_label_seq_id', [3, '322', '5%'], [3, '362', '5%'], [3, '372', '5%'], [3, '390', '5%'], [3, '429', '5%'], [3, '762', '5%']], ['16 end_auth_seq_id', [3, '303', '5%'], [3, '343', '5%'], [3, '353', '5%'], [3, '371', '5%'], [3, '410', '5%'], [3, '743', '5%']], ['19 details', [60, '?', '100%']], ['20 pdbx_PDB_helix_length', [12, '6', '20%'], [6, '5', '10%'], [6, '7', '10%'], [6, '9', '10%'], [6, '3', '10%'], [3, '10', '5%']]]]
tables(11) | (display() & shape()) | deref()
-------------------- _struct_conn -------------------- 0 conn_type_id 1 details 2 id 3 ptnr1_label_asym_id 4 ptnr1_label_atom_id 5 ptnr1_label_comp_id 6 ptnr1_label_seq_id 7 ptnr1_auth_asym_id 8 ptnr1_auth_comp_id 9 ptnr1_auth_seq_id 10 ptnr1_symmetry 11 ptnr2_label_asym_id 12 ptnr2_label_atom_id 13 ptnr2_label_comp_id 14 ptnr2_label_seq_id 15 ptnr2_auth_asym_id 16 ptnr2_auth_comp_id 17 ptnr2_auth_seq_id 18 ptnr2_symmetry 19 pdbx_ptnr1_PDB_ins_code 20 pdbx_ptnr1_label_alt_id 21 pdbx_ptnr1_standard_comp_id 22 pdbx_ptnr2_PDB_ins_code 23 pdbx_ptnr2_label_alt_id 24 pdbx_ptnr3_PDB_ins_code 25 pdbx_ptnr3_label_alt_id 26 pdbx_ptnr3_label_asym_id 27 pdbx_ptnr3_label_atom_id 28 pdbx_ptnr3_label_comp_id 29 pdbx_ptnr3_label_seq_id 30 pdbx_PDB_id 31 pdbx_dist_value 32 pdbx_value_order disulf ? disulf1 A SG CYS 150 A CYS 131 1_555 A SG CYS 185 A CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 310 A CYS 291 1_555 A SG CYS 320 A CYS 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf3 A SG CYS 355 A CYS 336 1_555 A SG CYS 380 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf4 A SG CYS 398 A CYS 379 1_555 A SG CYS 451 A CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf5 A SG CYS 410 A CYS 391 1_555 A SG CYS 544 A CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? disulf ? disulf6 A SG CYS 557 A CYS 538 1_555 A SG CYS 609 A CYS 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf7 A SG CYS 636 A CYS 617 1_555 A SG CYS 668 A CYS 649 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf8 A SG CYS 681 A CYS 662 1_555 A SG CYS 690 A CYS 671 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf9 A SG CYS 757 A CYS 738 1_555 A SG CYS 779 A CYS 760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ?
[None, [100, 33, 14]]
tables(11) | cuts(0, 1, 3, 4, 5, 7, 8, 10, 11, 12, 13, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32) | freqs.all() | deref()
-------------------- _struct_conn --------------------
[[['0 conn_type_id', [63, 'covale', '64%'], [36, 'disulf', '36%']], ['1 details', [99, '?', '100%']], ['3 ptnr1_label_asym_id', [28, 'A', '28%'], [28, 'B', '28%'], [28, 'C', '28%'], [1, 'D', '1%'], [1, 'E', '1%'], [1, 'F', '1%']], ['4 ptnr1_label_atom_id', [48, 'ND2', '48%'], [36, 'SG', '36%'], [15, 'O4', '15%']], ['5 ptnr1_label_comp_id', [48, 'ASN', '48%'], [36, 'CYS', '36%'], [15, 'NAG', '15%']], ['7 ptnr1_auth_asym_id', [28, 'A', '28%'], [28, 'B', '28%'], [28, 'C', '28%'], [1, 'D', '1%'], [1, 'E', '1%'], [1, 'F', '1%']], ['8 ptnr1_auth_comp_id', [48, 'ASN', '48%'], [36, 'CYS', '36%'], [15, 'NAG', '15%']], ['10 ptnr1_symmetry', [99, '1_555', '100%']], ['11 ptnr2_label_asym_id', [12, 'A', '12%'], [12, 'B', '12%'], [12, 'C', '12%'], [2, 'D', '2%'], [2, 'E', '2%'], [2, 'F', '2%']], ['12 ptnr2_label_atom_id', [63, 'C1', '64%'], [36, 'SG', '36%']], ['13 ptnr2_label_comp_id', [63, 'NAG', '64%'], [36, 'CYS', '36%']], ['15 ptnr2_auth_asym_id', [23, 'A', '23%'], [23, 'B', '23%'], [23, 'C', '23%'], [2, 'D', '2%'], [2, 'E', '2%'], [2, 'F', '2%']], ['16 ptnr2_auth_comp_id', [63, 'NAG', '64%'], [36, 'CYS', '36%']], ['18 ptnr2_symmetry', [99, '1_555', '100%']], ['19 pdbx_ptnr1_PDB_ins_code', [99, '?', '100%']], ['20 pdbx_ptnr1_label_alt_id', [99, '?', '100%']], ['21 pdbx_ptnr1_standard_comp_id', [99, '?', '100%']], ['22 pdbx_ptnr2_PDB_ins_code', [99, '?', '100%']], ['23 pdbx_ptnr2_label_alt_id', [99, '?', '100%']], ['24 pdbx_ptnr3_PDB_ins_code', [99, '?', '100%']], ['25 pdbx_ptnr3_label_alt_id', [99, '?', '100%']], ['26 pdbx_ptnr3_label_asym_id', [99, '?', '100%']], ['27 pdbx_ptnr3_label_atom_id', [99, '?', '100%']], ['28 pdbx_ptnr3_label_comp_id', [99, '?', '100%']], ['29 pdbx_ptnr3_label_seq_id', [99, '?', '100%']], ['30 pdbx_PDB_id', [99, '?', '100%']], ['32 pdbx_value_order', [99, '?', '100%']]], [['2 id', [1, 'disulf1', '1%'], [1, 'disulf2', '1%'], [1, 'disulf3', '1%'], [1, 'disulf4', '1%'], [1, 'disulf5', '1%'], [1, 'disulf6', '1%']], ['6 ptnr1_label_seq_id', [15, '.', '15%'], [3, '150', '3%'], [3, '310', '3%'], [3, '355', '3%'], [3, '398', '3%'], [3, '410', '3%']], ['9 ptnr1_auth_seq_id', [15, '1', '15%'], [3, '131', '3%'], [3, '291', '3%'], [3, '336', '3%'], [3, '379', '3%'], [3, '391', '3%']], ['14 ptnr2_label_seq_id', [63, '.', '64%'], [3, '185', '3%'], [3, '320', '3%'], [3, '380', '3%'], [3, '451', '3%'], [3, '544', '3%']], ['17 ptnr2_auth_seq_id', [15, '1', '15%'], [15, '2', '15%'], [3, '166', '3%'], [3, '301', '3%'], [3, '361', '3%'], [3, '432', '3%']], ['31 pdbx_dist_value', [13, '1.51', '13%'], [8, '1.499', '8%'], [6, '2.025', '6%'], [5, '1.507', '5%'], [5, '1.505', '5%'], [4, '2.022', '4%']]]]
tables(12) | display()
-------------------- _struct_conn_type -------------------- 0 criteria 1 id 2 reference ? disulf ? ? covale ?
tables(13) | (display() & shape()) | deref()
-------------------- _struct_sheet -------------------- 0 id 1 type 2 number_strands 3 details AA1 . 7 . AA2 . 7 . AA3 . 3 . AA4 . 3 . AA5 . 6 . AA6 . 5 . AA7 . 7 . AA8 . 5 . AA9 . 2 .
[None, [46, 4, 4]]
tables(13) | cuts(1, 2, 3) | freqs.all() | deref()
-------------------- _struct_sheet --------------------
[[['1 type', [45, '.', '100%']], ['2 number_strands', [12, '2', '27%'], [9, '3', '20%'], [9, '5', '20%'], [6, '7', '13%'], [6, '4', '13%'], [3, '6', '7%']], ['3 details', [45, '.', '100%']]], [['0 id', [1, 'AA1', '2%'], [1, 'AA2', '2%'], [1, 'AA3', '2%'], [1, 'AA4', '2%'], [1, 'AA5', '2%'], [1, 'AA6', '2%']]]]
tables(13) | cut(0) | batched(5) | deref()
-------------------- _struct_sheet --------------------
[['0 id', 'AA1', 'AA2', 'AA3', 'AA4'], ['AA5', 'AA6', 'AA7', 'AA8', 'AA9'], ['AB1', 'AB2', 'AB3', 'AB4', 'AB5'], ['AB6', 'AB7', 'AB8', 'AB9', 'AC1'], ['AC2', 'AC3', 'AC4', 'AC5', 'AC6'], ['AC7', 'AC8', 'AC9', 'AD1', 'AD2'], ['AD3', 'AD4', 'AD5', 'AD6', 'AD7'], ['AD8', 'AD9', 'AE1', 'AE2', 'AE3'], ['AE4', 'AE5', 'AE6', 'AE7', 'AE8']]
tables(14) | (display() & shape()) | deref()
-------------------- _struct_sheet_order -------------------- 0 sheet_id 1 range_id_1 2 range_id_2 3 offset 4 sense AA1 1 2 . anti-parallel AA1 2 3 . anti-parallel AA1 3 4 . anti-parallel AA1 4 5 . anti-parallel AA1 5 6 . anti-parallel AA1 6 7 . anti-parallel AA2 1 2 . parallel AA2 2 3 . anti-parallel AA2 3 4 . anti-parallel
[None, [136, 5, 10]]
tables(14) | cuts(3, 4) | freqs.all() | deref()
-------------------- _struct_sheet_order --------------------
[[['3 offset', [135, '.', '100%']], ['4 sense', [114, 'anti-parallel', '84%'], [21, 'parallel', '16%']]], [['0 sheet_id', [6, 'AA1', '4%'], [6, 'AA2', '4%'], [6, 'AA7', '4%'], [6, 'AB9', '4%'], [6, 'AC5', '4%'], [6, 'AD6', '4%']], ['1 range_id_1', [45, '1', '33%'], [33, '2', '24%'], [24, '3', '18%'], [18, '4', '13%'], [9, '5', '7%'], [6, '6', '4%']], ['2 range_id_2', [45, '2', '33%'], [33, '3', '24%'], [24, '4', '18%'], [18, '5', '13%'], [9, '6', '7%'], [6, '7', '4%']]]]
tables(15) | (display() & shape()) | deref()
-------------------- _struct_sheet_range -------------------- 0 sheet_id 1 id 2 beg_label_comp_id 3 beg_label_seq_id 4 pdbx_beg_PDB_ins_code 5 beg_label_asym_id 6 beg_label_entity_id 7 beg_auth_comp_id 8 beg_auth_seq_id 9 beg_auth_asym_id 10 end_label_comp_id 11 end_label_seq_id 12 pdbx_end_PDB_ins_code 13 end_label_asym_id 14 end_label_entity_id 15 end_auth_comp_id 16 end_auth_seq_id 17 end_auth_asym_id 18 symmetry AA1 1 TYR 47 . A 1 TYR 28 A ASN 49 . A 1 ASN 30 A ? AA1 2 ASN 80 . A 1 ASN 61 A PHE 84 . A 1 PHE 65 A ? AA1 3 VAL 109 . A 1 VAL 90 A GLU 115 . A 1 GLU 96 A ? AA1 4 ASN 207 . A 1 ASN 188 A ILE 216 . A 1 ILE 197 A ? AA1 5 TYR 219 . A 1 TYR 200 A PRO 228 . A 1 PRO 209 A ? AA1 6 GLU 243 . A 1 GLU 224 A LEU 248 . A 1 LEU 229 A ? AA1 7 TYR 284 . A 1 TYR 265 A TYR 288 . A 1 TYR 269 A ? AA2 8 VAL 61 . A 1 VAL 42 A PHE 62 . A 1 PHE 43 A ? AA2 9 SER 344 . C 1 SER 325 C ARG 347 . C 1 ARG 328 C ?
[None, [169, 19, 10]]
tables(15) | cuts(2, 4, 5, 6, 7, 9, 10, 12, 13, 14, 15, 17, 18) | freqs.all() | deref()
-------------------- _struct_sheet_range --------------------
[[['2 beg_label_comp_id', [24, 'VAL', '14%'], [18, 'ASN', '11%'], [18, 'ILE', '11%'], [12, 'TYR', '7%'], [12, 'LEU', '7%'], [12, 'GLN', '7%']], ['4 pdbx_beg_PDB_ins_code', [168, '.', '100%']], ['5 beg_label_asym_id', [56, 'A', '33%'], [56, 'C', '33%'], [56, 'B', '33%']], ['6 beg_label_entity_id', [168, '1', '100%']], ['7 beg_auth_comp_id', [24, 'VAL', '14%'], [18, 'ASN', '11%'], [18, 'ILE', '11%'], [12, 'TYR', '7%'], [12, 'LEU', '7%'], [12, 'GLN', '7%']], ['9 beg_auth_asym_id', [56, 'A', '33%'], [56, 'C', '33%'], [56, 'B', '33%']], ['10 end_label_comp_id', [15, 'ASN', '9%'], [15, 'PHE', '9%'], [15, 'ILE', '9%'], [15, 'ARG', '9%'], [15, 'THR', '9%'], [12, 'GLU', '7%']], ['12 pdbx_end_PDB_ins_code', [168, '.', '100%']], ['13 end_label_asym_id', [56, 'A', '33%'], [56, 'C', '33%'], [56, 'B', '33%']], ['14 end_label_entity_id', [168, '1', '100%']], ['15 end_auth_comp_id', [15, 'ASN', '9%'], [15, 'PHE', '9%'], [15, 'ILE', '9%'], [15, 'ARG', '9%'], [15, 'THR', '9%'], [12, 'GLU', '7%']], ['17 end_auth_asym_id', [56, 'A', '33%'], [56, 'C', '33%'], [56, 'B', '33%']], ['18 symmetry', [168, '?', '100%']]], [['0 sheet_id', [7, 'AA1', '4%'], [7, 'AA2', '4%'], [7, 'AA7', '4%'], [7, 'AB9', '4%'], [7, 'AC5', '4%'], [7, 'AD6', '4%']], ['1 id', [1, '1', '1%'], [1, '2', '1%'], [1, '3', '1%'], [1, '4', '1%'], [1, '5', '1%'], [1, '6', '1%']], ['3 beg_label_seq_id', [3, '47', '2%'], [3, '80', '2%'], [3, '109', '2%'], [3, '207', '2%'], [3, '219', '2%'], [3, '243', '2%']], ['8 beg_auth_seq_id', [3, '28', '2%'], [3, '61', '2%'], [3, '90', '2%'], [3, '188', '2%'], [3, '200', '2%'], [3, '224', '2%']], ['11 end_label_seq_id', [3, '49', '2%'], [3, '84', '2%'], [3, '115', '2%'], [3, '216', '2%'], [3, '228', '2%'], [3, '248', '2%']], ['16 end_auth_seq_id', [3, '30', '2%'], [3, '65', '2%'], [3, '96', '2%'], [3, '197', '2%'], [3, '209', '2%'], [3, '229', '2%']]]]
tables(16) | (display() & shape()) | deref()
-------------------- _pdbx_struct_sheet_hbond -------------------- 0 sheet_id 1 range_id_1 2 range_id_2 3 range_1_label_atom_id 4 range_1_label_comp_id 5 range_1_label_asym_id 6 range_1_label_seq_id 7 range_1_PDB_ins_code 8 range_1_auth_atom_id 9 range_1_auth_comp_id 10 range_1_auth_asym_id 11 range_1_auth_seq_id 12 range_2_label_atom_id 13 range_2_label_comp_id 14 range_2_label_asym_id 15 range_2_label_seq_id 16 range_2_PDB_ins_code 17 range_2_auth_atom_id 18 range_2_auth_comp_id 19 range_2_auth_asym_id 20 range_2_auth_seq_id AA1 1 2 N THR A 48 . N THR A 29 O VAL A 81 . O VAL A 62 AA1 2 3 N PHE A 84 . N PHE A 65 O TYR A 284 . O TYR A 265 AA1 3 4 O TYR A 285 . O TYR A 266 N ALA A 112 . N ALA A 93 AA1 4 5 N PHE A 111 . N PHE A 92 O PHE A 211 . O PHE A 192 AA1 5 6 N LEU A 208 . N LEU A 189 O THR A 227 . O THR A 208 AA1 6 7 N ILE A 222 . N ILE A 203 O LEU A 245 . O LEU A 226 AA2 1 2 N PHE A 62 . N PHE A 43 O PHE C 584 . O PHE C 565 AA2 2 3 N GLY C 585 . N GLY C 566 O ALA C 594 . O ALA C 575 AA2 3 4 N VAL C 595 . N VAL C 576 O LEU C 604 . O LEU C 585
[None, [136, 21, 10]]
tables(16) | cuts(1, 3, 4, 5, 7, 8, 9, 10, 12, 13, 14, 16, 17, 18, 19) | freqs.all() | deref()
-------------------- _pdbx_struct_sheet_hbond --------------------
[[['1 range_id_1', [45, '1', '33%'], [33, '2', '24%'], [24, '3', '18%'], [18, '4', '13%'], [9, '5', '7%'], [6, '6', '4%']], ['3 range_1_label_atom_id', [95, 'N', '70%'], [40, 'O', '30%']], ['4 range_1_label_comp_id', [24, 'LEU', '18%'], [19, 'ILE', '14%'], [18, 'VAL', '13%'], [17, 'PHE', '13%'], [9, 'GLU', '7%'], [7, 'THR', '5%']], ['5 range_1_label_asym_id', [47, 'A', '35%'], [45, 'B', '33%'], [43, 'C', '32%']], ['7 range_1_PDB_ins_code', [135, '.', '100%']], ['8 range_1_auth_atom_id', [95, 'N', '70%'], [40, 'O', '30%']], ['9 range_1_auth_comp_id', [24, 'LEU', '18%'], [19, 'ILE', '14%'], [18, 'VAL', '13%'], [17, 'PHE', '13%'], [9, 'GLU', '7%'], [7, 'THR', '5%']], ['10 range_1_auth_asym_id', [47, 'A', '35%'], [45, 'B', '33%'], [43, 'C', '32%']], ['12 range_2_label_atom_id', [95, 'O', '70%'], [40, 'N', '30%']], ['13 range_2_label_comp_id', [28, 'PHE', '21%'], [15, 'LEU', '11%'], [14, 'ILE', '10%'], [12, 'VAL', '9%'], [11, 'ALA', '8%'], [9, 'TYR', '7%']], ['14 range_2_label_asym_id', [47, 'C', '35%'], [45, 'B', '33%'], [43, 'A', '32%']], ['16 range_2_PDB_ins_code', [135, '.', '100%']], ['17 range_2_auth_atom_id', [95, 'O', '70%'], [40, 'N', '30%']], ['18 range_2_auth_comp_id', [28, 'PHE', '21%'], [15, 'LEU', '11%'], [14, 'ILE', '10%'], [12, 'VAL', '9%'], [11, 'ALA', '8%'], [9, 'TYR', '7%']], ['19 range_2_auth_asym_id', [47, 'C', '35%'], [45, 'B', '33%'], [43, 'A', '32%']]], [['0 sheet_id', [6, 'AA1', '4%'], [6, 'AA2', '4%'], [6, 'AA7', '4%'], [6, 'AB9', '4%'], [6, 'AC5', '4%'], [6, 'AD6', '4%']], ['2 range_id_2', [45, '2', '33%'], [33, '3', '24%'], [24, '4', '18%'], [18, '5', '13%'], [9, '6', '7%'], [6, '7', '4%']], ['6 range_1_label_seq_id', [6, '103', '4%'], [6, '744', '4%'], [3, '48', '2%'], [3, '84', '2%'], [3, '285', '2%'], [3, '111', '2%']], ['11 range_1_auth_seq_id', [6, '84', '4%'], [6, '725', '4%'], [3, '29', '2%'], [3, '65', '2%'], [3, '266', '2%'], [3, '92', '2%']], ['15 range_2_label_seq_id', [6, '257', '4%'], [6, '1081', '4%'], [3, '81', '2%'], [3, '284', '2%'], [3, '112', '2%'], [3, '211', '2%']], ['20 range_2_auth_seq_id', [6, '238', '4%'], [6, '1062', '4%'], [3, '62', '2%'], [3, '265', '2%'], [3, '93', '2%'], [3, '192', '2%']]]]
tables(17) | display()
-------------------- _atom_type -------------------- 0 symbol C N O S
tables(18) | (display() & shape()) | deref()
-------------------- _atom_site -------------------- 0 group_PDB 1 id 2 type_symbol 3 label_atom_id 4 label_comp_id 5 label_seq_id 6 label_alt_id 7 pdbx_PDB_ins_code 8 label_asym_id 9 label_entity_id 10 Cartn_x 11 Cartn_y 12 Cartn_z 13 occupancy 14 B_iso_or_equiv 15 pdbx_formal_charge 16 auth_atom_id 17 auth_comp_id 18 auth_seq_id 19 auth_asym_id 20 pdbx_PDB_model_num ATOM 1 N N ALA 46 . . A 1 171.646 251.874 224.877 1 34.23 ? N ALA 27 A 1 ATOM 2 C CA ALA 46 . . A 1 172.298 252.181 223.613 1 34.95 ? CA ALA 27 A 1 ATOM 3 C C ALA 46 . . A 1 173.53 251.298 223.427 1 34.25 ? C ALA 27 A 1 ATOM 4 O O ALA 46 . . A 1 174.195 250.943 224.405 1 34.3 ? O ALA 27 A 1 ATOM 5 C CB ALA 46 . . A 1 172.7 253.664 223.554 1 35.54 ? CB ALA 27 A 1 ATOM 6 N N TYR 47 . . A 1 173.816 250.939 222.166 1 34.21 ? N TYR 28 A 1 ATOM 7 C CA TYR 47 . . A 1 174.968 250.129 221.763 1 34.2 ? CA TYR 28 A 1 ATOM 8 C C TYR 47 . . A 1 175.652 250.729 220.561 1 34.22 ? C TYR 28 A 1 ATOM 9 O O TYR 47 . . A 1 175.009 251.379 219.736 1 34.22 ? O TYR 28 A 1
[None, [23695, 21, 11]]
tables(18) | cuts(0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 15, 16, 17, 19, 20) | freqs.all() | deref()
-------------------- _atom_site --------------------
[[['0 group_PDB', [22812, 'ATOM', '96%'], [882, 'HETATM', '4%']], ['2 type_symbol', [15087, 'C', '64%'], [4659, 'O', '20%'], [3849, 'N', '16%'], [99, 'S', '0%']], ['3 label_atom_id', [2916, 'N', '12%'], [2916, 'CA', '12%'], [2916, 'C', '12%'], [2916, 'O', '12%'], [2742, 'CB', '12%'], [1614, 'CG', '7%']], ['4 label_comp_id', [2145, 'PHE', '9%'], [1920, 'LEU', '8%'], [1728, 'ASN', '7%'], [1680, 'THR', '7%'], [1617, 'VAL', '7%'], [1512, 'TYR', '6%']], ['5 label_seq_id', [882, '.', '4%'], [42, '83', '0%'], [42, '123', '0%'], [42, '372', '0%'], [42, '455', '0%'], [42, '905', '0%']], ['6 label_alt_id', [23694, '.', '100%']], ['7 pdbx_PDB_ins_code', [23694, '.', '100%']], ['8 label_asym_id', [7604, 'A', '32%'], [7604, 'B', '32%'], [7604, 'C', '32%'], [28, 'D', '0%'], [28, 'E', '0%'], [28, 'F', '0%']], ['9 label_entity_id', [22812, '1', '96%'], [462, '3', '2%'], [420, '2', '2%']], ['13 occupancy', [23694, '1', '100%']], ['15 pdbx_formal_charge', [23694, '?', '100%']], ['16 auth_atom_id', [2916, 'N', '12%'], [2916, 'CA', '12%'], [2916, 'C', '12%'], [2916, 'O', '12%'], [2742, 'CB', '12%'], [1614, 'CG', '7%']], ['17 auth_comp_id', [2145, 'PHE', '9%'], [1920, 'LEU', '8%'], [1728, 'ASN', '7%'], [1680, 'THR', '7%'], [1617, 'VAL', '7%'], [1512, 'TYR', '6%']], ['19 auth_asym_id', [7758, 'A', '33%'], [7758, 'B', '33%'], [7758, 'C', '33%'], [28, 'D', '0%'], [28, 'E', '0%'], [28, 'F', '0%']], ['20 pdbx_PDB_model_num', [23694, '1', '100%']]], [['1 id', [1, '1', '0%'], [1, '2', '0%'], [1, '3', '0%'], [1, '4', '0%'], [1, '5', '0%'], [1, '6', '0%']], ['10 Cartn_x', [5, '217.745', '0%'], [5, '212.665', '0%'], [5, '213.833', '0%'], [4, '178.617', '0%'], [4, '198.79', '0%'], [4, '192.664', '0%']], ['11 Cartn_y', [5, '227.858', '0%'], [5, '207.91', '0%'], [4, '238.673', '0%'], [4, '221.933', '0%'], [4, '218.486', '0%'], [4, '214.158', '0%']], ['12 Cartn_z', [9, '218.979', '0%'], [9, '253.284', '0%'], [9, '244.276', '0%'], [9, '240.379', '0%'], [9, '218.235', '0%'], [9, '243.714', '0%']], ['14 B_iso_or_equiv', [33, '8.56', '0%'], [33, '8.05', '0%'], [30, '9.11', '0%'], [30, '8.34', '0%'], [27, '8.3', '0%'], [27, '7.31', '0%']], ['18 auth_seq_id', [210, '1', '1%'], [210, '2', '1%'], [42, '64', '0%'], [42, '104', '0%'], [42, '353', '0%'], [42, '436', '0%']]]]
tables(19) | (display() & shape()) | deref()
-------------------- _pdbx_poly_seq_scheme -------------------- 0 asym_id 1 entity_id 2 seq_id 3 mon_id 4 ndb_seq_num 5 pdb_seq_num 6 auth_seq_num 7 pdb_mon_id 8 auth_mon_id 9 pdb_strand_id 10 pdb_ins_code 11 hetero A 1 1 MET 1 -18 . . . A . n A 1 2 GLY 2 -17 . . . A . n A 1 3 ILE 3 -16 . . . A . n A 1 4 LEU 4 -15 . . . A . n A 1 5 PRO 5 -14 . . . A . n A 1 6 SER 6 -13 . . . A . n A 1 7 PRO 7 -12 . . . A . n A 1 8 GLY 8 -11 . . . A . n A 1 9 MET 9 -10 . . . A . n
[None, [3844, 12, 9]]
tables(19) | cuts(0, 1, 3, 6, 7, 8, 9, 10, 11) | freqs.all() | deref()
-------------------- _pdbx_poly_seq_scheme --------------------
[[['0 asym_id', [1281, 'A', '33%'], [1281, 'B', '33%'], [1281, 'C', '33%']], ['1 entity_id', [3843, '1', '100%']], ['3 mon_id', [330, 'LEU', '9%'], [300, 'SER', '8%'], [291, 'THR', '8%'], [282, 'VAL', '7%'], [279, 'GLY', '7%'], [267, 'ASN', '7%']], ['6 auth_seq_num', [927, '.', '24%'], [3, '27', '0%'], [3, '28', '0%'], [3, '29', '0%'], [3, '30', '0%'], [3, '31', '0%']], ['7 pdb_mon_id', [927, '.', '24%'], [240, 'THR', '6%'], [240, 'LEU', '6%'], [231, 'VAL', '6%'], [216, 'ASN', '6%'], [216, 'SER', '6%']], ['8 auth_mon_id', [927, '.', '24%'], [240, 'THR', '6%'], [240, 'LEU', '6%'], [231, 'VAL', '6%'], [216, 'ASN', '6%'], [216, 'SER', '6%']], ['9 pdb_strand_id', [1281, 'A', '33%'], [1281, 'B', '33%'], [1281, 'C', '33%']], ['10 pdb_ins_code', [3843, '.', '100%']], ['11 hetero', [3843, 'n', '100%']]], [['2 seq_id', [3, '1', '0%'], [3, '2', '0%'], [3, '3', '0%'], [3, '4', '0%'], [3, '5', '0%'], [3, '6', '0%']], ['4 ndb_seq_num', [3, '1', '0%'], [3, '2', '0%'], [3, '3', '0%'], [3, '4', '0%'], [3, '5', '0%'], [3, '6', '0%']], ['5 pdb_seq_num', [3, '-18', '0%'], [3, '-17', '0%'], [3, '-16', '0%'], [3, '-15', '0%'], [3, '-14', '0%'], [3, '-13', '0%']]]]
tables(20) | (display() & shape()) | deref()
-------------------- _pdbx_nonpoly_scheme -------------------- 0 asym_id 1 entity_id 2 mon_id 3 pdb_strand_id 4 ndb_seq_num 5 pdb_seq_num 6 auth_seq_num 7 pdb_mon_id 8 auth_mon_id 9 pdb_ins_code S 3 NAG A 1 1301 1329 NAG NAG . T 3 NAG A 1 1302 1334 NAG NAG . U 3 NAG A 1 1305 1339 NAG NAG . V 3 NAG A 1 1306 1342 NAG NAG . W 3 NAG A 1 1307 1343 NAG NAG . X 3 NAG A 1 1308 1346 NAG NAG . Y 3 NAG A 1 1309 1347 NAG NAG . Z 3 NAG A 1 1310 1348 NAG NAG . AA 3 NAG A 1 1311 1350 NAG NAG .
[None, [34, 10, 9]]
tables(20) | cuts(1, 2, 3, 4, 7, 8, 9) | freqs.all() | deref()
-------------------- _pdbx_nonpoly_scheme --------------------
[[['1 entity_id', [33, '3', '100%']], ['2 mon_id', [33, 'NAG', '100%']], ['3 pdb_strand_id', [11, 'A', '33%'], [11, 'B', '33%'], [11, 'C', '33%']], ['4 ndb_seq_num', [33, '1', '100%']], ['7 pdb_mon_id', [33, 'NAG', '100%']], ['8 auth_mon_id', [33, 'NAG', '100%']], ['9 pdb_ins_code', [33, '.', '100%']]], [['0 asym_id', [1, 'S', '3%'], [1, 'T', '3%'], [1, 'U', '3%'], [1, 'V', '3%'], [1, 'W', '3%'], [1, 'X', '3%']], ['5 pdb_seq_num', [3, '1301', '9%'], [3, '1302', '9%'], [3, '1305', '9%'], [3, '1306', '9%'], [3, '1307', '9%'], [3, '1308', '9%']], ['6 auth_seq_num', [3, '1329', '9%'], [3, '1334', '9%'], [3, '1339', '9%'], [3, '1342', '9%'], [3, '1343', '9%'], [3, '1346', '9%']]]]
# thumbnail
tables(21) | display()
-------------------- _pdbx_struct_assembly_prop -------------------- 0 biol_id 1 type 2 value 3 details 1 'ABSA (A^2)' 41790 . 1 MORE 34 . 1 'SSA (A^2)' 130680 .
tables(22) | display(None)
-------------------- _pdbx_audit_revision_history -------------------- 0 ordinal 1 data_content_type 2 major_revision 3 minor_revision 4 revision_date 1 'Structure model' 1 0 2020-03-11 2 'Structure model' 1 1 2020-03-25 3 'Structure model' 1 2 2020-04-01 4 'Structure model' 1 3 2020-04-29 5 'Structure model' 1 4 2020-05-06 6 'Structure model' 2 0 2020-07-29 7 'Structure model' 2 1 2021-01-27
tables(23) | display()
-------------------- _pdbx_audit_revision_details -------------------- 0 ordinal 1 revision_ordinal 2 data_content_type 3 provider 4 type 5 description 6 details 1 1 'Structure model' repository 'Initial release' . . 2 6 'Structure model' repository Remediation 'Carbohydrate remediation' .
tables(24) | display(None)
-------------------- _pdbx_audit_revision_group -------------------- 0 ordinal 1 revision_ordinal 2 data_content_type 3 group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Structure summary' 3 4 'Structure model' 'Database references' 4 5 'Structure model' 'Database references' 5 5 'Structure model' 'Source and taxonomy' 6 5 'Structure model' 'Structure summary' 7 6 'Structure model' 'Atomic model' 8 6 'Structure model' 'Data collection' 9 6 'Structure model' 'Derived calculations' 10 6 'Structure model' 'Structure summary' 11 7 'Structure model' 'Structure summary'
tables(25) | display(None)
-------------------- _pdbx_audit_revision_category -------------------- 0 ordinal 1 revision_ordinal 2 data_content_type 3 category 1 2 'Structure model' citation 2 3 'Structure model' entity 3 4 'Structure model' citation 4 5 'Structure model' entity_name_com 5 5 'Structure model' entity_src_gen 6 5 'Structure model' struct_ref 7 5 'Structure model' struct_ref_seq 8 5 'Structure model' struct_ref_seq_dif 9 6 'Structure model' atom_site 10 6 'Structure model' chem_comp 11 6 'Structure model' entity 12 6 'Structure model' pdbx_branch_scheme 13 6 'Structure model' pdbx_chem_comp_identifier 14 6 'Structure model' pdbx_entity_branch 15 6 'Structure model' pdbx_entity_branch_descriptor 16 6 'Structure model' pdbx_entity_branch_link 17 6 'Structure model' pdbx_entity_branch_list 18 6 'Structure model' pdbx_entity_nonpoly 19 6 'Structure model' pdbx_nonpoly_scheme 20 6 'Structure model' pdbx_struct_assembly_gen 21 6 'Structure model' struct_asym 22 6 'Structure model' struct_conn 23 6 'Structure model' struct_site 24 6 'Structure model' struct_site_gen 25 7 'Structure model' chem_comp 26 7 'Structure model' entity 27 7 'Structure model' entity_name_com
tables(26) | display(None)
-------------------- _pdbx_audit_revision_item -------------------- 0 ordinal 1 revision_ordinal 2 data_content_type 3 item 1 2 'Structure model' '_citation.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_ASTM' 4 2 'Structure model' '_citation.journal_id_CSD' 5 2 'Structure model' '_citation.journal_id_ISSN' 6 2 'Structure model' '_citation.pdbx_database_id_PubMed' 7 2 'Structure model' '_citation.title' 8 3 'Structure model' '_entity.pdbx_description' 9 4 'Structure model' '_citation.journal_volume' 10 4 'Structure model' '_citation.page_first' 11 5 'Structure model' '_entity_src_gen.gene_src_common_name' 12 5 'Structure model' '_entity_src_gen.pdbx_gene_src_gene' 13 5 'Structure model' '_struct_ref.db_code' 14 5 'Structure model' '_struct_ref.db_name' 15 5 'Structure model' '_struct_ref.pdbx_align_begin' 16 5 'Structure model' '_struct_ref.pdbx_db_accession' 17 5 'Structure model' '_struct_ref.pdbx_seq_one_letter_code' 18 5 'Structure model' '_struct_ref_seq.db_align_beg' 19 5 'Structure model' '_struct_ref_seq.db_align_end' 20 5 'Structure model' '_struct_ref_seq.pdbx_auth_seq_align_beg' 21 5 'Structure model' '_struct_ref_seq.pdbx_auth_seq_align_end' 22 5 'Structure model' '_struct_ref_seq.pdbx_db_accession' 23 5 'Structure model' '_struct_ref_seq.seq_align_beg' 24 5 'Structure model' '_struct_ref_seq.seq_align_end' 25 6 'Structure model' '_atom_site.B_iso_or_equiv' 26 6 'Structure model' '_atom_site.Cartn_x' 27 6 'Structure model' '_atom_site.Cartn_y' 28 6 'Structure model' '_atom_site.Cartn_z' 29 6 'Structure model' '_atom_site.auth_asym_id' 30 6 'Structure model' '_atom_site.auth_seq_id' 31 6 'Structure model' '_atom_site.label_asym_id' 32 6 'Structure model' '_atom_site.label_entity_id' 33 6 'Structure model' '_chem_comp.name' 34 6 'Structure model' '_pdbx_entity_nonpoly.entity_id' 35 6 'Structure model' '_pdbx_entity_nonpoly.name' 36 6 'Structure model' '_pdbx_struct_assembly_gen.asym_id_list' 37 6 'Structure model' '_struct_conn.pdbx_role' 38 6 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 39 6 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 40 6 'Structure model' '_struct_conn.ptnr1_label_asym_id' 41 6 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 42 6 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 43 6 'Structure model' '_struct_conn.ptnr2_label_asym_id' 44 7 'Structure model' '_chem_comp.pdbx_synonyms' 45 7 'Structure model' '_entity.pdbx_description' 46 7 'Structure model' '_entity_name_com.name'
tables(27) | display()
-------------------- _pdbx_validate_rmsd_bond -------------------- 0 id 1 PDB_model_num 2 auth_atom_id_1 3 auth_asym_id_1 4 auth_comp_id_1 5 auth_seq_id_1 6 PDB_ins_code_1 7 label_alt_id_1 8 auth_atom_id_2 9 auth_asym_id_2 10 auth_comp_id_2 11 auth_seq_id_2 12 PDB_ins_code_2 13 label_alt_id_2 14 bond_value 15 bond_target_value 16 bond_deviation 17 bond_standard_deviation 18 linker_flag 1 1 CB A CYS 525 . . SG A CYS 525 . . 1.935 1.818 0.117 0.017 N 2 1 CB B CYS 525 . . SG B CYS 525 . . 1.935 1.818 0.117 0.017 N 3 1 CB C CYS 525 . . SG C CYS 525 . . 1.935 1.818 0.117 0.017 N
tables(28) | display(None)
-------------------- _pdbx_validate_rmsd_angle -------------------- 0 id 1 PDB_model_num 2 auth_atom_id_1 3 auth_asym_id_1 4 auth_comp_id_1 5 auth_seq_id_1 6 PDB_ins_code_1 7 label_alt_id_1 8 auth_atom_id_2 9 auth_asym_id_2 10 auth_comp_id_2 11 auth_seq_id_2 12 PDB_ins_code_2 13 label_alt_id_2 14 auth_atom_id_3 15 auth_asym_id_3 16 auth_comp_id_3 17 auth_seq_id_3 18 PDB_ins_code_3 19 label_alt_id_3 20 angle_value 21 angle_target_value 22 angle_deviation 23 angle_standard_deviation 24 linker_flag 1 1 CB A TYR 451 . . CG A TYR 451 . . CD2 A TYR 451 . . 116.93 121 -4.07 0.6000000000000001 N 2 1 CB A TYR 904 . . CG A TYR 904 . . CD2 A TYR 904 . . 116.68 121 -4.32 0.6000000000000001 N 3 1 CB B TYR 451 . . CG B TYR 451 . . CD2 B TYR 451 . . 116.89 121 -4.11 0.6000000000000001 N 4 1 CB B TYR 904 . . CG B TYR 904 . . CD2 B TYR 904 . . 116.65 121 -4.3500000000000005 0.6000000000000001 N 5 1 CB C TYR 451 . . CG C TYR 451 . . CD2 C TYR 451 . . 116.92 121 -4.08 0.6000000000000001 N 6 1 CB C TYR 904 . . CG C TYR 904 . . CD2 C TYR 904 . . 116.66 121 -4.34 0.6000000000000001 N
tables(29) | (display() & shape()) | deref()
-------------------- _pdbx_validate_torsion -------------------- 0 id 1 PDB_model_num 2 auth_comp_id 3 auth_asym_id 4 auth_seq_id 5 PDB_ins_code 6 label_alt_id 7 phi 8 psi 1 1 PHE A 32 . . 51.72 -117.39 2 1 PHE A 59 . . 59.97 19.87 3 1 ASN A 87 . . 53.910000000000004 -124.39 4 1 SER A 98 . . -143.63 17.8 5 1 ALA A 123 . . 64.89 -104.45 6 1 LEU A 441 . . -142.34 -54.36 7 1 THR A 618 . . -131.72 -75.07000000000001 8 1 ASP A 663 . . -118 -80.93 9 1 CYS A 1032 . . -139.61 -52.46
[None, [41, 9, 4]]
tables(29) | cuts(1, 2, 3, 5, 6) | freqs.all() | deref()
-------------------- _pdbx_validate_torsion --------------------
[[['1 PDB_model_num', [40, '1', '100%']], ['2 auth_comp_id', [6, 'LEU', '15%'], [6, 'ASP', '15%'], [6, 'CYS', '15%'], [4, 'PHE', '10%'], [3, 'ASN', '8%'], [3, 'SER', '8%']], ['3 auth_asym_id', [14, 'A', '35%'], [13, 'B', '32%'], [13, 'C', '32%']], ['5 PDB_ins_code', [40, '.', '100%']], ['6 label_alt_id', [40, '.', '100%']]], [['0 id', [1, '1', '2%'], [1, '2', '2%'], [1, '3', '2%'], [1, '4', '2%'], [1, '5', '2%'], [1, '6', '2%']], ['4 auth_seq_id', [3, '32', '8%'], [3, '87', '8%'], [3, '98', '8%'], [3, '123', '8%'], [3, '441', '8%'], [3, '618', '8%']], ['7 phi', [2, '-142.34', '5%'], [2, '-118', '5%'], [2, '-139.61', '5%'], [2, '58.22', '5%'], [2, '-119.14', '5%'], [2, '-106.63', '5%']], ['8 psi', [2, '-80.93', '5%'], [2, '15.64', '5%'], [2, '79.73', '5%'], [2, '-104.46000000000001', '5%'], [1, '-117.39', '2%'], [1, '19.87', '2%']]]]
tables(30) | (display() & shape()) | deref()
-------------------- _pdbx_unobs_or_zero_occ_residues -------------------- 0 id 1 polymer_flag 2 occupancy_flag 3 PDB_model_num 4 auth_asym_id 5 auth_comp_id 6 auth_seq_id 7 PDB_ins_code 8 label_asym_id 9 label_comp_id 10 label_seq_id 1 y 1 1 A MET -18 ? A MET 1 2 y 1 1 A GLY -17 ? A GLY 2 3 y 1 1 A ILE -16 ? A ILE 3 4 y 1 1 A LEU -15 ? A LEU 4 5 y 1 1 A PRO -14 ? A PRO 5 6 y 1 1 A SER -13 ? A SER 6 7 y 1 1 A PRO -12 ? A PRO 7 8 y 1 1 A GLY -11 ? A GLY 8 9 y 1 1 A MET -10 ? A MET 9
[None, [928, 11, 4]]
tables(30) | cuts(1, 2, 3, 4, 5, 7, 8, 9) | freqs.all() | deref()
-------------------- _pdbx_unobs_or_zero_occ_residues --------------------
[[['1 polymer_flag', [927, 'y', '100%']], ['2 occupancy_flag', [927, '1', '100%']], ['3 PDB_model_num', [927, '1', '100%']], ['4 auth_asym_id', [309, 'A', '33%'], [309, 'B', '33%'], [309, 'C', '33%']], ['5 auth_comp_id', [105, 'GLY', '11%'], [90, 'LEU', '10%'], [84, 'SER', '9%'], [57, 'ALA', '6%'], [51, 'VAL', '6%'], [51, 'THR', '6%']], ['7 PDB_ins_code', [927, '?', '100%']], ['8 label_asym_id', [309, 'A', '33%'], [309, 'B', '33%'], [309, 'C', '33%']], ['9 label_comp_id', [105, 'GLY', '11%'], [90, 'LEU', '10%'], [84, 'SER', '9%'], [57, 'ALA', '6%'], [51, 'VAL', '6%'], [51, 'THR', '6%']]], [['0 id', [1, '1', '0%'], [1, '2', '0%'], [1, '3', '0%'], [1, '4', '0%'], [1, '5', '0%'], [1, '6', '0%']], ['6 auth_seq_id', [3, '-18', '0%'], [3, '-17', '0%'], [3, '-16', '0%'], [3, '-15', '0%'], [3, '-14', '0%'], [3, '-13', '0%']], ['10 label_seq_id', [3, '1', '0%'], [3, '2', '0%'], [3, '3', '0%'], [3, '4', '0%'], [3, '5', '0%'], [3, '6', '0%']]]]
tables(31) | display(None)
-------------------- _em_software -------------------- 0 id 1 category 2 details 3 name 4 version 5 image_processing_id 6 fitting_id 7 imaging_id 1 'PARTICLE SELECTION' . Warp . 1 . . 2 'IMAGE ACQUISITION' . Leginon 3.3000000000000003 . . 1 3 MASKING . . . . . . 4 'CTF CORRECTION' . . . 1 . . 5 'LAYERLINE INDEXING' . . . . . . 6 'DIFFRACTION INDEXING' . . . . . . 7 'MODEL FITTING' . . . . . . 8 'MODEL REFINEMENT' . . . . . . 9 OTHER . . . . . . 10 'INITIAL EULER ASSIGNMENT' . . . 1 . . 11 'FINAL EULER ASSIGNMENT' . . . 1 . . 12 CLASSIFICATION . RELION . 1 . . 13 RECONSTRUCTION . cryoSPARC . 1 . .
tables(32) | (display(None) & shape()) | deref()
-------------------- _pdbx_branch_scheme -------------------- 0 entity_id 1 hetero 2 asym_id 3 mon_id 4 num 5 pdb_asym_id 6 pdb_seq_num 7 pdb_mon_id 8 auth_asym_id 9 auth_seq_num 10 auth_mon_id 2 n D NAG 1 D 1 NAG A 1337 NAG 2 n D NAG 2 D 2 NAG A 1338 NAG 2 n E NAG 1 E 1 NAG A 1355 NAG 2 n E NAG 2 E 2 NAG A 1356 NAG 2 n F NAG 1 F 1 NAG A 1358 NAG 2 n F NAG 2 F 2 NAG A 1359 NAG 2 n G NAG 1 G 1 NAG A 1368 NAG 2 n G NAG 2 G 2 NAG A 1369 NAG 2 n H NAG 1 H 1 NAG A 1373 NAG 2 n H NAG 2 H 2 NAG A 1374 NAG 2 n I NAG 1 I 1 NAG B 1337 NAG 2 n I NAG 2 I 2 NAG B 1338 NAG 2 n J NAG 1 J 1 NAG B 1355 NAG 2 n J NAG 2 J 2 NAG B 1356 NAG 2 n K NAG 1 K 1 NAG B 1358 NAG 2 n K NAG 2 K 2 NAG B 1359 NAG 2 n L NAG 1 L 1 NAG B 1368 NAG 2 n L NAG 2 L 2 NAG B 1369 NAG 2 n M NAG 1 M 1 NAG B 1373 NAG 2 n M NAG 2 M 2 NAG B 1374 NAG 2 n N NAG 1 N 1 NAG C 1337 NAG 2 n N NAG 2 N 2 NAG C 1338 NAG 2 n O NAG 1 O 1 NAG C 1355 NAG 2 n O NAG 2 O 2 NAG C 1356 NAG 2 n P NAG 1 P 1 NAG C 1358 NAG 2 n P NAG 2 P 2 NAG C 1359 NAG 2 n Q NAG 1 Q 1 NAG C 1368 NAG 2 n Q NAG 2 Q 2 NAG C 1369 NAG 2 n R NAG 1 R 1 NAG C 1373 NAG 2 n R NAG 2 R 2 NAG C 1374 NAG
[None, [31, 11, 11]]
tables(33) | display()
-------------------- _pdbx_chem_comp_identifier -------------------- 0 comp_id 1 identifier 2 type 3 program 4 program_version NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1
tables(34) | display()
-------------------- _pdbx_entity_branch_descriptor --------------------
0 entity_id 1 descriptor 2 type 3 program 4 program_version 5 ordinal
2 DGlcpNAcb1-4DGlcpNAcb1- 'glycam condensed sequence' GMML 1.0 1
2 WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1 wurcs PDB2Glycan 1.1.0 2
2 '[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}' linucs PDB-CARE ? 3
tables(35) | display()
-------------------- _pdbx_entity_branch_list -------------------- 0 entity_id 1 hetero 2 comp_id 3 num 2 n NAG 1 2 n NAG 2