data_1Y8P # _model_server_result.job_id Vvyec_diY3z8KU2VJTdw1Q _model_server_result.datetime_utc '2024-11-04 23:23:28' _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 1y8p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":373}' # _entry.id 1Y8P # _exptl.entry_id 1Y8P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 208.341 _entity.id 6 _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 1Y8P _cell.length_a 120.904 _cell.length_b 120.904 _cell.length_c 240.085 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Y8P _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,G,H,I _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 -120.904 0 120.0425 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id G _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 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? metalc ? metalc2 A O PHE 35 A PHE 22 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.822 ? metalc ? metalc3 A OD1 ASN 72 A ASN 59 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.964 ? metalc ? metalc4 A OD1 ASN 264 A ASN 251 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc5 A O LEU 313 A LEU 300 1_555 E K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? metalc ? metalc6 A O ASN 315 A ASN 302 1_555 E K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.019 ? metalc ? metalc7 A O TYR 318 A TYR 305 1_555 E K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.077 ? metalc ? metalc8 A O GLY 338 A GLY 325 1_555 E K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.916 ? metalc ? metalc9 A O PHE 385 A PHE 372 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc10 C MG MG . A MG 501 1_555 F O2B ATP . A ATP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.892 ? metalc ? metalc11 C MG MG . A MG 501 1_555 F O1G ATP . A ATP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc12 C MG MG . A MG 501 1_555 F O2A ATP . A ATP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc13 C MG MG . A MG 501 1_555 H O HOH . A HOH 535 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc14 E K K . A K 503 1_555 F O1A ATP . A ATP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? # _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 326 n n C1 OXT RED sing 327 n n C1 C2 RED sing 328 n n OXT HO RED sing 329 n n C2 C3 RED sing 330 n n C2 H22 RED sing 331 n n C2 H21 RED sing 332 n n C3 C4 RED sing 333 n n C3 H32 RED sing 334 n n C3 H31 RED sing 335 n n C4 C5 RED sing 336 n n C4 H42 RED sing 337 n n C4 H41 RED sing 338 n n C5 C6 RED sing 339 n n C5 H52 RED sing 340 n n C5 H51 RED sing 341 n n C6 C7 RED sing 342 n n C6 S6 RED sing 343 n n C6 H6 RED sing 344 n n C7 C8 RED sing 345 n n C7 H72 RED sing 346 n n C7 H71 RED sing 347 n n C8 S8 RED sing 348 n n C8 H82 RED sing 349 n n C8 H81 RED sing 350 n n S8 H8S RED sing 351 n n S6 H6S RED sing 352 n n # _atom_sites.entry_id 1Y8P _atom_sites.fract_transf_matrix[1][1] 0.008271 _atom_sites.fract_transf_matrix[1][2] 0.004775 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009551 _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] 0.004165 _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 MG A 1 501 1 MG MG . D 4 K A 1 502 2 K K . E 4 K A 1 503 3 K K . F 5 ATP A 1 504 1 ATP ATP . G 6 RED B 1 373 173 RED LPA . H 7 HOH A 1 505 1 HOH WAT . H 7 HOH A 2 506 2 HOH WAT . H 7 HOH A 3 507 3 HOH WAT . H 7 HOH A 4 508 4 HOH WAT . H 7 HOH A 5 509 5 HOH WAT . H 7 HOH A 6 510 7 HOH WAT . H 7 HOH A 7 511 8 HOH WAT . H 7 HOH A 8 512 10 HOH WAT . H 7 HOH A 9 513 11 HOH WAT . H 7 HOH A 10 514 12 HOH WAT . H 7 HOH A 11 515 13 HOH WAT . H 7 HOH A 12 516 14 HOH WAT . H 7 HOH A 13 517 15 HOH WAT . H 7 HOH A 14 518 16 HOH WAT . H 7 HOH A 15 519 17 HOH WAT . H 7 HOH A 16 520 18 HOH WAT . H 7 HOH A 17 521 19 HOH WAT . H 7 HOH A 18 522 20 HOH WAT . H 7 HOH A 19 523 21 HOH WAT . H 7 HOH A 20 524 22 HOH WAT . H 7 HOH A 21 525 23 HOH WAT . H 7 HOH A 22 526 24 HOH WAT . H 7 HOH A 23 527 25 HOH WAT . H 7 HOH A 24 528 26 HOH WAT . H 7 HOH A 25 529 27 HOH WAT . H 7 HOH A 26 530 28 HOH WAT . H 7 HOH A 27 531 29 HOH WAT . H 7 HOH A 28 532 30 HOH WAT . H 7 HOH A 29 533 31 HOH WAT . H 7 HOH A 30 534 32 HOH WAT . H 7 HOH A 31 535 33 HOH WAT . H 7 HOH A 32 536 34 HOH WAT . H 7 HOH A 33 537 35 HOH WAT . H 7 HOH A 34 538 36 HOH WAT . H 7 HOH A 35 539 37 HOH WAT . H 7 HOH A 36 540 38 HOH WAT . H 7 HOH A 37 541 39 HOH WAT . H 7 HOH A 38 542 40 HOH WAT . H 7 HOH A 39 543 41 HOH WAT . H 7 HOH A 40 544 42 HOH WAT . H 7 HOH A 41 545 43 HOH WAT . H 7 HOH A 42 546 44 HOH WAT . H 7 HOH A 43 547 45 HOH WAT . H 7 HOH A 44 548 46 HOH WAT . H 7 HOH A 45 549 47 HOH WAT . H 7 HOH A 46 550 48 HOH WAT . H 7 HOH A 47 551 49 HOH WAT . H 7 HOH A 48 552 50 HOH WAT . H 7 HOH A 49 553 51 HOH WAT . H 7 HOH A 50 554 52 HOH WAT . H 7 HOH A 51 555 53 HOH WAT . H 7 HOH A 52 556 55 HOH WAT . H 7 HOH A 53 557 56 HOH WAT . I 7 HOH B 1 6 6 HOH WAT . I 7 HOH B 2 9 9 HOH WAT . I 7 HOH B 3 54 54 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 . . . G 6 -79.567 0.846 85.148 1 54.9 ? C1 RED 373 B 1 HETATM 2 O O1 RED . . . G 6 -79.584 -0.099 85.935 1 56.25 ? O1 RED 373 B 1 HETATM 3 C C2 RED . . . G 6 -79.968 2.244 85.528 1 56.08 ? C2 RED 373 B 1 HETATM 4 C C3 RED . . . G 6 -78.981 2.686 86.578 1 56.35 ? C3 RED 373 B 1 HETATM 5 C C4 RED . . . G 6 -79.427 4.033 87.075 1 58.8 ? C4 RED 373 B 1 HETATM 6 C C5 RED . . . G 6 -78.717 4.269 88.389 1 62.28 ? C5 RED 373 B 1 HETATM 7 C C6 RED . . . G 6 -77.229 4.48 88.15 1 64.05 ? C6 RED 373 B 1 HETATM 8 C C7 RED . . . G 6 -76.524 4.103 89.446 1 66.77 ? C7 RED 373 B 1 HETATM 9 C C8 RED . . . G 6 -75.846 5.284 90.118 1 69.16 ? C8 RED 373 B 1 HETATM 10 S S8 RED . . . G 6 -74.24 5.432 89.31 1 73.07 ? S8 RED 373 B 1 HETATM 11 S S6 RED . . . G 6 -76.949 6.19 87.698 1 63.46 ? S6 RED 373 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 11 #