data_4OGU # _model_server_result.job_id S8NWP8-tjlYi4mzPMp68bQ _model_server_result.datetime_utc '2024-10-19 19:40:28' _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 4ogu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":404}' # _entry.id 4OGU # _exptl.entry_id 4OGU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 246.092 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE' _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 90 _cell.entry_id 4OGU _cell.length_a 111.21 _cell.length_b 111.21 _cell.length_c 67.27 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4OGU _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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 _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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 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 OD2 ASP 125 A ASP 103 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc2 A OD1 ASP 125 A ASP 103 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? metalc ? metalc3 A OD2 ASP 129 A ASP 107 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc4 A OD2 ASP 129 A ASP 107 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc5 A OD2 ASP 265 A ASP 243 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc6 B MG MG . A MG 401 1_555 F O2 210 . A 210 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc7 B MG MG . A MG 401 1_555 F O10 210 . A 210 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc8 B MG MG . A MG 401 1_555 G O HOH . A HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.935 ? metalc ? metalc9 B MG MG . A MG 401 1_555 G O HOH . A HOH 593 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc10 B MG MG . A MG 401 1_555 G O HOH . A HOH 594 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.895 ? metalc ? metalc11 C MG MG . A MG 402 1_555 F O9 210 . A 210 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc12 C MG MG . A MG 402 1_555 F O5 210 . A 210 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc13 C MG MG . A MG 402 1_555 G O HOH . A HOH 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc14 C MG MG . A MG 402 1_555 G O HOH . A HOH 591 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc15 C MG MG . A MG 402 1_555 G O HOH . A HOH 592 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc16 D MG MG . A MG 403 1_555 F O10 210 . A 210 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc17 D MG MG . A MG 403 1_555 G O HOH . A HOH 586 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc18 D MG MG . A MG 403 1_555 G O HOH . A HOH 587 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? metalc ? metalc19 D MG MG . A MG 403 1_555 G O HOH . A HOH 588 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? # _chem_comp.formula 'C5 H12 O7 P2' _chem_comp.formula_weight 246.092 _chem_comp.id IPE _chem_comp.mon_nstd_flag . _chem_comp.name '3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'ISOPENTENYL PYROPHOSPHATE' # 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 IPE sing 196 n n C1 C2 IPE sing 197 n n C1 H11 IPE sing 198 n n C1 H12 IPE sing 199 n n O1 PA IPE sing 200 n n C2 C3 IPE sing 201 n n C2 H21 IPE sing 202 n n C2 H22 IPE sing 203 n n C3 C4 IPE doub 204 n n C3 C5 IPE sing 205 n n C4 H41 IPE sing 206 n n C4 H42 IPE sing 207 n n C5 H51 IPE sing 208 n n C5 H52 IPE sing 209 n n C5 H53 IPE sing 210 n n PA O1A IPE doub 211 n n PA O2A IPE sing 212 n n PA O3A IPE sing 213 n n O2A H2A IPE sing 214 n n O3A PB IPE sing 215 n n PB O1B IPE sing 216 n n PB O2B IPE doub 217 n n PB O3B IPE sing 218 n n O1B H1B IPE sing 219 n n O3B H3B IPE sing 220 n n # _atom_sites.entry_id 4OGU _atom_sites.fract_transf_matrix[1][1] 0.008992 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008992 _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] 0.014865 _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 MG A 1 401 907 MG MG . C 2 MG A 1 402 908 MG MG . D 2 MG A 1 403 909 MG MG . E 3 IPE A 1 404 900 IPE IPE . F 4 210 A 1 405 901 210 210 . G 5 HOH A 1 501 3 HOH HOH . G 5 HOH A 2 502 4 HOH HOH . G 5 HOH A 3 503 5 HOH HOH . G 5 HOH A 4 504 6 HOH HOH . G 5 HOH A 5 505 7 HOH HOH . G 5 HOH A 6 506 8 HOH HOH . G 5 HOH A 7 507 9 HOH HOH . G 5 HOH A 8 508 10 HOH HOH . G 5 HOH A 9 509 13 HOH HOH . G 5 HOH A 10 510 14 HOH HOH . G 5 HOH A 11 511 15 HOH HOH . G 5 HOH A 12 512 16 HOH HOH . G 5 HOH A 13 513 17 HOH HOH . G 5 HOH A 14 514 18 HOH HOH . G 5 HOH A 15 515 19 HOH HOH . G 5 HOH A 16 516 20 HOH HOH . G 5 HOH A 17 517 21 HOH HOH . G 5 HOH A 18 518 22 HOH HOH . G 5 HOH A 19 519 23 HOH HOH . G 5 HOH A 20 520 24 HOH HOH . G 5 HOH A 21 521 25 HOH HOH . G 5 HOH A 22 522 26 HOH HOH . G 5 HOH A 23 523 27 HOH HOH . G 5 HOH A 24 524 28 HOH HOH . G 5 HOH A 25 525 29 HOH HOH . G 5 HOH A 26 526 30 HOH HOH . G 5 HOH A 27 527 31 HOH HOH . G 5 HOH A 28 528 32 HOH HOH . G 5 HOH A 29 529 33 HOH HOH . G 5 HOH A 30 530 34 HOH HOH . G 5 HOH A 31 531 35 HOH HOH . G 5 HOH A 32 532 36 HOH HOH . G 5 HOH A 33 533 37 HOH HOH . G 5 HOH A 34 534 38 HOH HOH . G 5 HOH A 35 535 39 HOH HOH . G 5 HOH A 36 536 40 HOH HOH . G 5 HOH A 37 537 41 HOH HOH . G 5 HOH A 38 538 44 HOH HOH . G 5 HOH A 39 539 45 HOH HOH . G 5 HOH A 40 540 46 HOH HOH . G 5 HOH A 41 541 49 HOH HOH . G 5 HOH A 42 542 51 HOH HOH . G 5 HOH A 43 543 52 HOH HOH . G 5 HOH A 44 544 53 HOH HOH . G 5 HOH A 45 545 55 HOH HOH . G 5 HOH A 46 546 56 HOH HOH . G 5 HOH A 47 547 57 HOH HOH . G 5 HOH A 48 548 58 HOH HOH . G 5 HOH A 49 549 60 HOH HOH . G 5 HOH A 50 550 62 HOH HOH . G 5 HOH A 51 551 65 HOH HOH . G 5 HOH A 52 552 66 HOH HOH . G 5 HOH A 53 553 70 HOH HOH . G 5 HOH A 54 554 73 HOH HOH . G 5 HOH A 55 555 77 HOH HOH . G 5 HOH A 56 556 78 HOH HOH . G 5 HOH A 57 557 80 HOH HOH . G 5 HOH A 58 558 83 HOH HOH . G 5 HOH A 59 559 84 HOH HOH . G 5 HOH A 60 560 87 HOH HOH . G 5 HOH A 61 561 88 HOH HOH . G 5 HOH A 62 562 90 HOH HOH . G 5 HOH A 63 563 91 HOH HOH . G 5 HOH A 64 564 93 HOH HOH . G 5 HOH A 65 565 95 HOH HOH . G 5 HOH A 66 566 96 HOH HOH . G 5 HOH A 67 567 97 HOH HOH . G 5 HOH A 68 568 102 HOH HOH . G 5 HOH A 69 569 104 HOH HOH . G 5 HOH A 70 570 105 HOH HOH . G 5 HOH A 71 571 106 HOH HOH . G 5 HOH A 72 572 109 HOH HOH . G 5 HOH A 73 573 110 HOH HOH . G 5 HOH A 74 574 114 HOH HOH . G 5 HOH A 75 575 115 HOH HOH . G 5 HOH A 76 576 118 HOH HOH . G 5 HOH A 77 577 119 HOH HOH . G 5 HOH A 78 578 124 HOH HOH . G 5 HOH A 79 579 125 HOH HOH . G 5 HOH A 80 580 126 HOH HOH . G 5 HOH A 81 581 130 HOH HOH . G 5 HOH A 82 582 131 HOH HOH . G 5 HOH A 83 583 132 HOH HOH . G 5 HOH A 84 584 136 HOH HOH . G 5 HOH A 85 585 137 HOH HOH . G 5 HOH A 86 586 139 HOH HOH . G 5 HOH A 87 587 140 HOH HOH . G 5 HOH A 88 588 141 HOH HOH . G 5 HOH A 89 589 142 HOH HOH . G 5 HOH A 90 590 143 HOH HOH . G 5 HOH A 91 591 144 HOH HOH . G 5 HOH A 92 592 145 HOH HOH . G 5 HOH A 93 593 146 HOH HOH . G 5 HOH A 94 594 147 HOH HOH . G 5 HOH A 95 595 148 HOH HOH . G 5 HOH A 96 596 149 HOH HOH . G 5 HOH A 97 597 150 HOH HOH . G 5 HOH A 98 598 151 HOH HOH . G 5 HOH A 99 599 154 HOH HOH . G 5 HOH A 100 600 155 HOH HOH . G 5 HOH A 101 601 156 HOH HOH . G 5 HOH A 102 602 157 HOH HOH . G 5 HOH A 103 603 158 HOH HOH . G 5 HOH A 104 604 159 HOH HOH . G 5 HOH A 105 605 160 HOH HOH . G 5 HOH A 106 606 161 HOH HOH . G 5 HOH A 107 607 162 HOH HOH . G 5 HOH A 108 608 163 HOH HOH . G 5 HOH A 109 609 164 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 IPE . . . E 3 10.482 34.204 -6.013 1 60.77 ? C1 IPE 404 A 1 HETATM 2 O O1 IPE . . . E 3 9.157 33.836 -5.855 1 63.26 ? O1 IPE 404 A 1 HETATM 3 C C2 IPE . . . E 3 11.015 34.141 -7.401 1 59.18 ? C2 IPE 404 A 1 HETATM 4 C C3 IPE . . . E 3 10.295 33.295 -8.407 1 57.03 ? C3 IPE 404 A 1 HETATM 5 C C4 IPE . . . E 3 10.667 31.847 -8.416 1 56.4 ? C4 IPE 404 A 1 HETATM 6 C C5 IPE . . . E 3 10.161 33.901 -9.758 1 56.07 ? C5 IPE 404 A 1 HETATM 7 P PA IPE . . . E 3 8.14 34.729 -5.069 1 61.42 ? PA IPE 404 A 1 HETATM 8 O O1A IPE . . . E 3 7.819 35.966 -5.887 1 60.64 ? O1A IPE 404 A 1 HETATM 9 O O2A IPE . . . E 3 6.889 33.922 -4.885 1 61.84 ? O2A IPE 404 A 1 HETATM 10 O O3A IPE . . . E 3 8.791 35.084 -3.695 1 57.11 ? O3A IPE 404 A 1 HETATM 11 P PB IPE . . . E 3 8.106 35.127 -2.29 1 54.72 ? PB IPE 404 A 1 HETATM 12 O O1B IPE . . . E 3 9.054 35.951 -1.431 1 49.36 ? O1B IPE 404 A 1 HETATM 13 O O2B IPE . . . E 3 6.742 35.814 -2.316 1 56.06 ? O2B IPE 404 A 1 HETATM 14 O O3B IPE . . . E 3 7.935 33.738 -1.717 1 50.26 ? O3B IPE 404 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 14 #