data_7YVA # _model_server_result.job_id y40i9kw1gCgH96txVv4HtQ _model_server_result.datetime_utc '2024-11-15 04:58:53' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 7yva # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":402}' # _entry.id 7YVA # _exptl.entry_id 7YVA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 206.326 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'LIPOIC ACID' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 96.33 _cell.angle_gamma 90 _cell.entry_id 7YVA _cell.length_a 159.181 _cell.length_b 56.622 _cell.length_c 81.839 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7YVA _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A NE2 HIS 110 A HIS 109 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc2 A OE1 GLU 174 A GLU 173 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc3 A OE2 GLU 174 A GLU 173 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc4 A NE2 HIS 226 A HIS 225 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc5 A ND1 HIS 265 A HIS 264 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc6 B NE2 HIS 110 B HIS 109 1_555 D ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc7 B OE1 GLU 174 B GLU 173 1_555 D ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc8 B OE2 GLU 174 B GLU 173 1_555 D ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? metalc ? metalc9 B NE2 HIS 226 B HIS 225 1_555 D ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc10 B ND1 HIS 265 B HIS 264 1_555 D ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? # _chem_comp.formula 'C8 H14 O2 S2' _chem_comp.formula_weight 206.326 _chem_comp.id LPA _chem_comp.mon_nstd_flag . _chem_comp.name 'LIPOIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '5-[(3R)-1,2-dithiolan-3-yl]pentanoic acid' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C2 C1 LPA sing 203 n n C1 O2 LPA doub 204 n n C1 O1 LPA sing 205 n n O1 HO1 LPA sing 206 n n C3 C2 LPA sing 207 n n C2 H2 LPA sing 208 n n C2 H2A LPA sing 209 n n C4 C3 LPA sing 210 n n C3 H3 LPA sing 211 n n C3 H3A LPA sing 212 n n C5 C4 LPA sing 213 n n C4 H4 LPA sing 214 n n C4 H4A LPA sing 215 n n C6 C5 LPA sing 216 n n C5 H5 LPA sing 217 n n C5 H5A LPA sing 218 n n C7 C6 LPA sing 219 n n C6 S6 LPA sing 220 n n C6 H6 LPA sing 221 n n S8 S6 LPA sing 222 n n C8 C7 LPA sing 223 n n C7 H7 LPA sing 224 n n C7 H7A LPA sing 225 n n C8 S8 LPA sing 226 n n C8 H8 LPA sing 227 n n C8 H8A LPA sing 228 n n # _atom_sites.entry_id 7YVA _atom_sites.fract_transf_matrix[1][1] 0.006282 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000697 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017661 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.012294 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 ZN A 1 401 401 ZN ZN . D 2 ZN B 1 401 401 ZN ZN . E 3 LPA B 1 402 501 LPA LPA . F 4 EDO B 1 403 502 EDO EDO . G 4 EDO B 1 404 503 EDO EDO . H 5 HOH A 1 501 96 HOH HOH . H 5 HOH A 2 502 54 HOH HOH . H 5 HOH A 3 503 47 HOH HOH . H 5 HOH A 4 504 104 HOH HOH . H 5 HOH A 5 505 68 HOH HOH . H 5 HOH A 6 506 18 HOH HOH . H 5 HOH A 7 507 53 HOH HOH . H 5 HOH A 8 508 42 HOH HOH . H 5 HOH A 9 509 62 HOH HOH . H 5 HOH A 10 510 40 HOH HOH . H 5 HOH A 11 511 57 HOH HOH . H 5 HOH A 12 512 77 HOH HOH . H 5 HOH A 13 513 103 HOH HOH . H 5 HOH A 14 514 16 HOH HOH . H 5 HOH A 15 515 24 HOH HOH . H 5 HOH A 16 516 17 HOH HOH . H 5 HOH A 17 517 11 HOH HOH . H 5 HOH A 18 518 101 HOH HOH . H 5 HOH A 19 519 61 HOH HOH . H 5 HOH A 20 520 99 HOH HOH . H 5 HOH A 21 521 22 HOH HOH . H 5 HOH A 22 522 78 HOH HOH . H 5 HOH A 23 523 1 HOH HOH . H 5 HOH A 24 524 70 HOH HOH . H 5 HOH A 25 525 84 HOH HOH . H 5 HOH A 26 526 64 HOH HOH . H 5 HOH A 27 527 66 HOH HOH . H 5 HOH A 28 528 55 HOH HOH . H 5 HOH A 29 529 39 HOH HOH . H 5 HOH A 30 530 13 HOH HOH . H 5 HOH A 31 531 48 HOH HOH . H 5 HOH A 32 532 37 HOH HOH . H 5 HOH A 33 533 46 HOH HOH . H 5 HOH A 34 534 97 HOH HOH . H 5 HOH A 35 535 35 HOH HOH . H 5 HOH A 36 536 87 HOH HOH . H 5 HOH A 37 537 91 HOH HOH . H 5 HOH A 38 538 52 HOH HOH . H 5 HOH A 39 539 60 HOH HOH . H 5 HOH A 40 540 9 HOH HOH . H 5 HOH A 41 541 29 HOH HOH . H 5 HOH A 42 542 41 HOH HOH . H 5 HOH A 43 543 38 HOH HOH . H 5 HOH A 44 544 32 HOH HOH . H 5 HOH A 45 545 102 HOH HOH . H 5 HOH A 46 546 49 HOH HOH . H 5 HOH A 47 547 63 HOH HOH . H 5 HOH A 48 548 27 HOH HOH . H 5 HOH A 49 549 79 HOH HOH . H 5 HOH A 50 550 81 HOH HOH . H 5 HOH A 51 551 34 HOH HOH . H 5 HOH A 52 552 36 HOH HOH . H 5 HOH A 53 553 8 HOH HOH . H 5 HOH A 54 554 100 HOH HOH . H 5 HOH A 55 555 5 HOH HOH . H 5 HOH A 56 556 30 HOH HOH . H 5 HOH A 57 557 74 HOH HOH . H 5 HOH A 58 558 10 HOH HOH . H 5 HOH A 59 559 33 HOH HOH . H 5 HOH A 60 560 93 HOH HOH . H 5 HOH A 61 561 67 HOH HOH . H 5 HOH A 62 562 107 HOH HOH . I 5 HOH B 1 501 106 HOH HOH . I 5 HOH B 2 502 105 HOH HOH . I 5 HOH B 3 503 20 HOH HOH . I 5 HOH B 4 504 14 HOH HOH . I 5 HOH B 5 505 28 HOH HOH . I 5 HOH B 6 506 44 HOH HOH . I 5 HOH B 7 507 31 HOH HOH . I 5 HOH B 8 508 15 HOH HOH . I 5 HOH B 9 509 73 HOH HOH . I 5 HOH B 10 510 7 HOH HOH . I 5 HOH B 11 511 4 HOH HOH . I 5 HOH B 12 512 65 HOH HOH . I 5 HOH B 13 513 58 HOH HOH . I 5 HOH B 14 514 23 HOH HOH . I 5 HOH B 15 515 80 HOH HOH . I 5 HOH B 16 516 19 HOH HOH . I 5 HOH B 17 517 59 HOH HOH . I 5 HOH B 18 518 95 HOH HOH . I 5 HOH B 19 519 25 HOH HOH . I 5 HOH B 20 520 94 HOH HOH . I 5 HOH B 21 521 69 HOH HOH . I 5 HOH B 22 522 75 HOH HOH . I 5 HOH B 23 523 83 HOH HOH . I 5 HOH B 24 524 43 HOH HOH . I 5 HOH B 25 525 26 HOH HOH . I 5 HOH B 26 526 72 HOH HOH . I 5 HOH B 27 527 89 HOH HOH . I 5 HOH B 28 528 56 HOH HOH . I 5 HOH B 29 529 98 HOH HOH . I 5 HOH B 30 530 3 HOH HOH . I 5 HOH B 31 531 76 HOH HOH . I 5 HOH B 32 532 86 HOH HOH . I 5 HOH B 33 533 71 HOH HOH . I 5 HOH B 34 534 45 HOH HOH . I 5 HOH B 35 535 2 HOH HOH . I 5 HOH B 36 536 88 HOH HOH . I 5 HOH B 37 537 90 HOH HOH . I 5 HOH B 38 538 12 HOH HOH . I 5 HOH B 39 539 51 HOH HOH . I 5 HOH B 40 540 108 HOH HOH . I 5 HOH B 41 541 82 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 LPA . . . E 3 -17.352 0.425 41.984 1 78.13 ? C1 LPA 402 B 1 HETATM 2 O O1 LPA . . . E 3 -16.504 -0.457 42.36 1 78.13 ? O1 LPA 402 B 1 HETATM 3 C C2 LPA . . . E 3 -18.661 0.695 42.739 1 78.94 ? C2 LPA 402 B 1 HETATM 4 O O2 LPA . . . E 3 -17.103 1.104 40.947 1 78.23 ? O2 LPA 402 B 1 HETATM 5 C C3 LPA . . . E 3 -19.609 1.471 41.816 1 80.13 ? C3 LPA 402 B 1 HETATM 6 C C4 LPA . . . E 3 -20.826 1.981 42.574 1 83.27 ? C4 LPA 402 B 1 HETATM 7 C C5 LPA . . . E 3 -21.901 2.558 41.626 1 83.76 ? C5 LPA 402 B 1 HETATM 8 C C6 LPA . . . E 3 -22.396 1.633 40.748 1 84.24 ? C6 LPA 402 B 1 HETATM 9 S S6 LPA . . . E 3 -23.961 1.317 40.843 1 91.08 ? S6 LPA 402 B 1 HETATM 10 C C7 LPA . . . E 3 -21.917 2.553 39.086 1 78.43 ? C7 LPA 402 B 1 HETATM 11 C C8 LPA . . . E 3 -23.232 3.32 38.899 1 78.39 ? C8 LPA 402 B 1 HETATM 12 S S8 LPA . . . E 3 -24.557 2.157 39.134 1 89.89 ? S8 LPA 402 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 12 #