data_3OYX # _model_server_result.job_id 5jYVXQwuZuzLfptjuvLZxg _model_server_result.datetime_utc '2024-10-12 19:24:37' _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 3oyx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 3OYX # _exptl.entry_id 3OYX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 74.035 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'GLYOXYLIC ACID' _entity.pdbx_number_of_molecules 2 _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 3OYX _cell.length_a 155.023 _cell.length_b 155.023 _cell.length_c 141.787 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3OYX _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA hexameric 6 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M 1 1,2,3 A,B,C,D,E,F,G,H,I,J,K,L,M 2 1,2,3,4,5,6 # 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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 141.787 5 'crystal symmetry operation' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 141.787 6 'crystal symmetry operation' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 141.787 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N 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 OE1 GLU 158 A GLU 158 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc2 A O MET 173 A MET 173 1_555 K K K . A K 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc3 A O LYS 175 A LYS 175 1_555 K K K . A K 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc4 A O PRO 176 A PRO 176 1_555 L K K . A K 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? metalc ? metalc5 A O ASN 178 A ASN 178 1_555 K K K . A K 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? metalc ? metalc6 A OD1 ASN 178 A ASN 178 1_555 K K K . A K 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.874 ? metalc ? metalc7 A O ASN 178 A ASN 178 1_555 L K K . A K 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.835 ? metalc ? metalc8 A OD1 ASN 179 A ASN 179 1_555 L K K . A K 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.711 ? metalc ? metalc9 A OE2 GLU 181 A GLU 181 1_555 K K K . A K 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? metalc ? metalc10 A OE1 GLU 181 A GLU 181 1_555 K K K . A K 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.021 ? metalc ? metalc11 A OD2 ASP 192 A ASP 192 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? metalc ? metalc12 A OG SER 217 A SER 217 1_555 J K K . A K 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? metalc ? metalc13 A O SER 217 A SER 217 1_555 J K K . A K 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.313 ? metalc ? metalc14 A OG SER 221 A SER 221 1_555 J K K . A K 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.036 ? metalc ? metalc15 A O GLY 252 A GLY 252 1_555 J K K . A K 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.978 ? metalc ? metalc16 M O HOH . A HOH 439 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc17 M O HOH . A HOH 440 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc18 M O HOH . A HOH 476 1_555 L K K . A K 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.065 ? metalc ? metalc19 M O HOH . A HOH 499 1_555 K K K . A K 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? metalc ? metalc20 B O1 GLV . A GLV 501 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? metalc ? metalc21 B O3 GLV . A GLV 501 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? # _chem_comp.formula 'C2 H2 O3' _chem_comp.formula_weight 74.035 _chem_comp.id GLV _chem_comp.mon_nstd_flag . _chem_comp.name 'GLYOXYLIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYOXALATE;GLYOXYLATE # 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 GLV doub 120 n n C1 C2 GLV sing 121 n n C1 H1 GLV sing 122 n n C2 O2 GLV doub 123 n n C2 O3 GLV sing 124 n n O3 HO3 GLV sing 125 n n # _atom_sites.entry_id 3OYX _atom_sites.fract_transf_matrix[1][1] 0.006451 _atom_sites.fract_transf_matrix[1][2] 0.003724 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007449 _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] 0.007053 _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 B 2 GLV A 1 501 501 GLV GLV . C 2 GLV A 1 502 502 GLV GLV . D 3 MG A 1 601 601 MG MG . E 4 CL A 1 701 701 CL CL . F 4 CL A 1 702 702 CL CL . G 4 CL A 1 703 703 CL CL . H 4 CL A 1 704 704 CL CL . I 4 CL A 1 705 705 CL CL . J 5 K A 1 801 801 K K . K 5 K A 1 802 802 K K . L 5 K A 1 803 803 K K . M 6 HOH A 1 434 1 HOH HOH . M 6 HOH A 2 435 2 HOH HOH . M 6 HOH A 3 436 3 HOH HOH . M 6 HOH A 4 437 4 HOH HOH . M 6 HOH A 5 438 5 HOH HOH . M 6 HOH A 6 439 6 HOH HOH . M 6 HOH A 7 440 7 HOH HOH . M 6 HOH A 8 441 8 HOH HOH . M 6 HOH A 9 442 9 HOH HOH . M 6 HOH A 10 443 10 HOH HOH . M 6 HOH A 11 444 11 HOH HOH . M 6 HOH A 12 445 12 HOH HOH . M 6 HOH A 13 446 13 HOH HOH . M 6 HOH A 14 447 14 HOH HOH . M 6 HOH A 15 448 15 HOH HOH . M 6 HOH A 16 449 16 HOH HOH . M 6 HOH A 17 450 17 HOH HOH . M 6 HOH A 18 451 18 HOH HOH . M 6 HOH A 19 452 19 HOH HOH . M 6 HOH A 20 453 20 HOH HOH . M 6 HOH A 21 454 21 HOH HOH . M 6 HOH A 22 455 22 HOH HOH . M 6 HOH A 23 456 23 HOH HOH . M 6 HOH A 24 457 24 HOH HOH . M 6 HOH A 25 458 25 HOH HOH . M 6 HOH A 26 459 26 HOH HOH . M 6 HOH A 27 460 27 HOH HOH . M 6 HOH A 28 461 28 HOH HOH . M 6 HOH A 29 462 29 HOH HOH . M 6 HOH A 30 463 30 HOH HOH . M 6 HOH A 31 464 31 HOH HOH . M 6 HOH A 32 465 32 HOH HOH . M 6 HOH A 33 466 33 HOH HOH . M 6 HOH A 34 467 34 HOH HOH . M 6 HOH A 35 468 35 HOH HOH . M 6 HOH A 36 469 36 HOH HOH . M 6 HOH A 37 470 37 HOH HOH . M 6 HOH A 38 471 38 HOH HOH . M 6 HOH A 39 472 39 HOH HOH . M 6 HOH A 40 473 40 HOH HOH . M 6 HOH A 41 474 41 HOH HOH . M 6 HOH A 42 475 42 HOH HOH . M 6 HOH A 43 476 43 HOH HOH . M 6 HOH A 44 477 44 HOH HOH . M 6 HOH A 45 478 45 HOH HOH . M 6 HOH A 46 479 46 HOH HOH . M 6 HOH A 47 480 47 HOH HOH . M 6 HOH A 48 481 48 HOH HOH . M 6 HOH A 49 482 49 HOH HOH . M 6 HOH A 50 483 50 HOH HOH . M 6 HOH A 51 484 51 HOH HOH . M 6 HOH A 52 485 52 HOH HOH . M 6 HOH A 53 486 53 HOH HOH . M 6 HOH A 54 487 54 HOH HOH . M 6 HOH A 55 488 55 HOH HOH . M 6 HOH A 56 489 56 HOH HOH . M 6 HOH A 57 490 57 HOH HOH . M 6 HOH A 58 491 58 HOH HOH . M 6 HOH A 59 492 59 HOH HOH . M 6 HOH A 60 493 60 HOH HOH . M 6 HOH A 61 494 61 HOH HOH . M 6 HOH A 62 495 62 HOH HOH . M 6 HOH A 63 496 63 HOH HOH . M 6 HOH A 64 497 64 HOH HOH . M 6 HOH A 65 498 65 HOH HOH . M 6 HOH A 66 499 66 HOH HOH . M 6 HOH A 67 500 67 HOH HOH . M 6 HOH A 68 503 68 HOH HOH . M 6 HOH A 69 504 69 HOH HOH . M 6 HOH A 70 505 70 HOH HOH . M 6 HOH A 71 506 71 HOH HOH . M 6 HOH A 72 507 72 HOH HOH . M 6 HOH A 73 508 73 HOH HOH . M 6 HOH A 74 509 74 HOH HOH . M 6 HOH A 75 510 75 HOH HOH . M 6 HOH A 76 511 76 HOH HOH . M 6 HOH A 77 512 77 HOH HOH . M 6 HOH A 78 513 78 HOH HOH . M 6 HOH A 79 514 79 HOH HOH . M 6 HOH A 80 515 80 HOH HOH . M 6 HOH A 81 516 81 HOH HOH . M 6 HOH A 82 517 82 HOH HOH . M 6 HOH A 83 518 83 HOH HOH . M 6 HOH A 84 519 84 HOH HOH . M 6 HOH A 85 520 85 HOH HOH . M 6 HOH A 86 521 86 HOH HOH . M 6 HOH A 87 522 87 HOH HOH . M 6 HOH A 88 523 88 HOH HOH . M 6 HOH A 89 524 89 HOH HOH . M 6 HOH A 90 525 90 HOH HOH . M 6 HOH A 91 526 91 HOH HOH . M 6 HOH A 92 527 92 HOH HOH . M 6 HOH A 93 528 93 HOH HOH . M 6 HOH A 94 529 94 HOH HOH . M 6 HOH A 95 530 95 HOH HOH . M 6 HOH A 96 531 96 HOH HOH . M 6 HOH A 97 532 97 HOH HOH . M 6 HOH A 98 533 98 HOH HOH . M 6 HOH A 99 534 99 HOH HOH . M 6 HOH A 100 535 100 HOH HOH . M 6 HOH A 101 536 101 HOH HOH . M 6 HOH A 102 537 102 HOH HOH . M 6 HOH A 103 538 103 HOH HOH . M 6 HOH A 104 539 104 HOH HOH . M 6 HOH A 105 540 105 HOH HOH . M 6 HOH A 106 541 106 HOH HOH . M 6 HOH A 107 542 107 HOH HOH . M 6 HOH A 108 543 108 HOH HOH . M 6 HOH A 109 544 109 HOH HOH . M 6 HOH A 110 545 110 HOH HOH . M 6 HOH A 111 546 111 HOH HOH . M 6 HOH A 112 547 112 HOH HOH . M 6 HOH A 113 548 113 HOH HOH . M 6 HOH A 114 549 114 HOH HOH . M 6 HOH A 115 550 115 HOH HOH . M 6 HOH A 116 551 116 HOH HOH . M 6 HOH A 117 552 117 HOH HOH . M 6 HOH A 118 553 118 HOH HOH . M 6 HOH A 119 554 119 HOH HOH . M 6 HOH A 120 555 120 HOH HOH . M 6 HOH A 121 556 121 HOH HOH . M 6 HOH A 122 557 122 HOH HOH . M 6 HOH A 123 558 123 HOH HOH . M 6 HOH A 124 559 124 HOH HOH . M 6 HOH A 125 560 125 HOH HOH . M 6 HOH A 126 561 126 HOH HOH . M 6 HOH A 127 562 127 HOH HOH . M 6 HOH A 128 563 128 HOH HOH . M 6 HOH A 129 564 129 HOH HOH . M 6 HOH A 130 565 130 HOH HOH . M 6 HOH A 131 566 131 HOH HOH . M 6 HOH A 132 567 132 HOH HOH . M 6 HOH A 133 568 133 HOH HOH . M 6 HOH A 134 569 134 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 GLV . . . B 2 -20.632 0.186 47.566 1 38.12 ? C1 GLV 501 A 1 HETATM 2 O O1 GLV . . . B 2 -21.461 0.525 48.418 1 42.28 ? O1 GLV 501 A 1 HETATM 3 C C2 GLV . . . B 2 -20.011 1.325 46.877 1 42.24 ? C2 GLV 501 A 1 HETATM 4 O O2 GLV . . . B 2 -19.336 1.102 45.875 1 41.03 ? O2 GLV 501 A 1 HETATM 5 O O3 GLV . . . B 2 -20.145 2.569 47.408 1 38.02 ? O3 GLV 501 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 5 #