data_1Y8N # _model_server_result.job_id HawR0MZE3qwwzF_TsTy0hQ _model_server_result.datetime_utc '2024-11-05 16:25:51' _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 1y8n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":373}' # _entry.id 1Y8N # _exptl.entry_id 1Y8N _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 208.341 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIHYDROLIPOIC 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 90 _cell.angle_gamma 120 _cell.entry_id 1Y8N _cell.length_a 120.806 _cell.length_b 120.806 _cell.length_c 238.587 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Y8N _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 11_455 -x+y-1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 -120.806 0 119.2935 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 O SER 33 A SER 20 1_555 C K K . A K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? metalc ? metalc2 A O PHE 35 A PHE 22 1_555 C K K . A K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? metalc ? metalc3 A OD1 ASN 72 A ASN 59 1_555 C K K . A K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.618 ? metalc ? metalc4 A O PHE 385 A PHE 372 1_555 C K K . A K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? # _chem_comp.formula 'C8 H16 O2 S2' _chem_comp.formula_weight 208.341 _chem_comp.id RED _chem_comp.mon_nstd_flag . _chem_comp.name 'DIHYDROLIPOIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C1 O1 RED doub 277 n n C1 OXT RED sing 278 n n C1 C2 RED sing 279 n n OXT HO RED sing 280 n n C2 C3 RED sing 281 n n C2 H22 RED sing 282 n n C2 H21 RED sing 283 n n C3 C4 RED sing 284 n n C3 H32 RED sing 285 n n C3 H31 RED sing 286 n n C4 C5 RED sing 287 n n C4 H42 RED sing 288 n n C4 H41 RED sing 289 n n C5 C6 RED sing 290 n n C5 H52 RED sing 291 n n C5 H51 RED sing 292 n n C6 C7 RED sing 293 n n C6 S6 RED sing 294 n n C6 H6 RED sing 295 n n C7 C8 RED sing 296 n n C7 H72 RED sing 297 n n C7 H71 RED sing 298 n n C8 S8 RED sing 299 n n C8 H82 RED sing 300 n n C8 H81 RED sing 301 n n S8 H8S RED sing 302 n n S6 H6S RED sing 303 n n # _atom_sites.entry_id 1Y8N _atom_sites.fract_transf_matrix[1][1] 0.008278 _atom_sites.fract_transf_matrix[1][2] 0.004779 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009558 _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] 0.004191 _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 3 K A 1 501 1 K K . D 4 RED B 1 373 173 RED LPA . E 5 HOH A 1 502 1 HOH WAT . E 5 HOH A 2 503 2 HOH WAT . E 5 HOH A 3 504 3 HOH WAT . E 5 HOH A 4 505 4 HOH WAT . E 5 HOH A 5 506 5 HOH WAT . E 5 HOH A 6 507 6 HOH WAT . E 5 HOH A 7 508 7 HOH WAT . E 5 HOH A 8 509 8 HOH WAT . E 5 HOH A 9 510 9 HOH WAT . E 5 HOH A 10 511 10 HOH WAT . E 5 HOH A 11 512 11 HOH WAT . E 5 HOH A 12 513 13 HOH WAT . E 5 HOH A 13 514 14 HOH WAT . E 5 HOH A 14 515 15 HOH WAT . E 5 HOH A 15 516 16 HOH WAT . E 5 HOH A 16 517 17 HOH WAT . E 5 HOH A 17 518 18 HOH WAT . E 5 HOH A 18 519 19 HOH WAT . E 5 HOH A 19 520 20 HOH WAT . E 5 HOH A 20 521 21 HOH WAT . E 5 HOH A 21 522 22 HOH WAT . E 5 HOH A 22 523 23 HOH WAT . E 5 HOH A 23 524 24 HOH WAT . E 5 HOH A 24 525 25 HOH WAT . E 5 HOH A 25 526 26 HOH WAT . E 5 HOH A 26 527 27 HOH WAT . E 5 HOH A 27 528 28 HOH WAT . E 5 HOH A 28 529 29 HOH WAT . E 5 HOH A 29 530 31 HOH WAT . E 5 HOH A 30 531 32 HOH WAT . E 5 HOH A 31 532 34 HOH WAT . E 5 HOH A 32 533 35 HOH WAT . E 5 HOH A 33 534 36 HOH WAT . E 5 HOH A 34 535 37 HOH WAT . E 5 HOH A 35 536 38 HOH WAT . E 5 HOH A 36 537 39 HOH WAT . E 5 HOH A 37 538 40 HOH WAT . E 5 HOH A 38 539 42 HOH WAT . E 5 HOH A 39 540 43 HOH WAT . E 5 HOH A 40 541 44 HOH WAT . E 5 HOH A 41 542 45 HOH WAT . E 5 HOH A 42 543 46 HOH WAT . E 5 HOH A 43 544 48 HOH WAT . E 5 HOH A 44 545 49 HOH WAT . E 5 HOH A 45 546 50 HOH WAT . E 5 HOH A 46 547 51 HOH WAT . E 5 HOH A 47 548 52 HOH WAT . E 5 HOH A 48 549 53 HOH WAT . F 5 HOH B 1 12 12 HOH WAT . F 5 HOH B 2 30 30 HOH WAT . F 5 HOH B 3 33 33 HOH WAT . F 5 HOH B 4 41 41 HOH WAT . F 5 HOH B 5 47 47 HOH WAT . # 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 RED . . . D 4 -79.135 1.679 85.087 1 67.87 ? C1 RED 373 B 1 HETATM 2 O O1 RED . . . D 4 -78.598 0.731 85.675 1 67.37 ? O1 RED 373 B 1 HETATM 3 C C2 RED . . . D 4 -79.307 3.087 85.623 1 69.02 ? C2 RED 373 B 1 HETATM 4 C C3 RED . . . D 4 -78.145 3.433 86.537 1 71.13 ? C3 RED 373 B 1 HETATM 5 C C4 RED . . . D 4 -78.456 4.699 87.333 1 72.59 ? C4 RED 373 B 1 HETATM 6 C C5 RED . . . D 4 -77.442 4.888 88.461 1 72.94 ? C5 RED 373 B 1 HETATM 7 C C6 RED . . . D 4 -76.08 5.349 87.961 1 74.1 ? C6 RED 373 B 1 HETATM 8 C C7 RED . . . D 4 -75.174 5.423 89.169 1 73.98 ? C7 RED 373 B 1 HETATM 9 C C8 RED . . . D 4 -74.305 6.662 89.188 1 75.36 ? C8 RED 373 B 1 HETATM 10 S S8 RED . . . D 4 -72.637 5.977 89.199 1 77.87 ? S8 RED 373 B 1 HETATM 11 S S6 RED . . . D 4 -76.238 6.966 87.197 1 75.95 ? S6 RED 373 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 11 #