data_6PGN # _model_server_result.job_id Shwq5id_6_Zod-8BtCbpag _model_server_result.datetime_utc '2024-11-24 14:00:09' _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 6pgn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 6PGN # _exptl.entry_id 6PGN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 314.209 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'GERANYL 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 120 _cell.entry_id 6PGN _cell.length_a 116.662 _cell.length_b 116.662 _cell.length_c 43.681 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PGN _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 C _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 OE1 GLU 184 A GLU 184 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc2 B MG MG . A MG 401 1_555 C O1A GPP . A GPP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc3 B MG MG . A MG 401 1_555 C O3B GPP . A GPP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc4 B MG MG . A MG 401 1_555 D O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc5 B MG MG . A MG 401 1_555 D O HOH . A HOH 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc6 B MG MG . A MG 401 1_555 D O HOH . A HOH 617 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? # _chem_comp.formula 'C10 H20 O7 P2' _chem_comp.formula_weight 314.209 _chem_comp.id GPP _chem_comp.mon_nstd_flag . _chem_comp.name 'GERANYL DIPHOSPHATE' _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 GPP sing 129 n n C1 C2 GPP sing 130 n n C1 H11 GPP sing 131 n n C1 H12 GPP sing 132 n n O1 PA GPP sing 133 n n C2 C3 GPP doub 134 e n C2 H2 GPP sing 135 n n C3 C4 GPP sing 136 n n C3 C5 GPP sing 137 n n C4 H41 GPP sing 138 n n C4 H42 GPP sing 139 n n C4 H43 GPP sing 140 n n C5 C6 GPP sing 141 n n C5 H51 GPP sing 142 n n C5 H52 GPP sing 143 n n C6 C7 GPP sing 144 n n C6 H61 GPP sing 145 n n C6 H62 GPP sing 146 n n C7 C8 GPP doub 147 n n C7 H7 GPP sing 148 n n C8 C9 GPP sing 149 n n C8 C10 GPP sing 150 n n C9 H91 GPP sing 151 n n C9 H92 GPP sing 152 n n C9 H93 GPP sing 153 n n C10 H101 GPP sing 154 n n C10 H102 GPP sing 155 n n C10 H103 GPP sing 156 n n PA O1A GPP doub 157 n n PA O2A GPP sing 158 n n PA O3A GPP sing 159 n n O2A HOA2 GPP sing 160 n n O3A PB GPP sing 161 n n PB O1B GPP doub 162 n n PB O2B GPP sing 163 n n PB O3B GPP sing 164 n n O2B HOB2 GPP sing 165 n n O3B HOB3 GPP sing 166 n n # _atom_sites.entry_id 6PGN _atom_sites.fract_transf_matrix[1][1] 0.008572 _atom_sites.fract_transf_matrix[1][2] 0.004949 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009898 _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] 0.022893 _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 1 401 301 MG MG . C 3 GPP A 1 402 300 GPP GPP . D 4 HOH A 1 501 12 HOH HOH . D 4 HOH A 2 502 91 HOH HOH . D 4 HOH A 3 503 17 HOH HOH . D 4 HOH A 4 504 68 HOH HOH . D 4 HOH A 5 505 144 HOH HOH . D 4 HOH A 6 506 44 HOH HOH . D 4 HOH A 7 507 119 HOH HOH . D 4 HOH A 8 508 64 HOH HOH . D 4 HOH A 9 509 92 HOH HOH . D 4 HOH A 10 510 89 HOH HOH . D 4 HOH A 11 511 168 HOH HOH . D 4 HOH A 12 512 208 HOH HOH . D 4 HOH A 13 513 110 HOH HOH . D 4 HOH A 14 514 112 HOH HOH . D 4 HOH A 15 515 41 HOH HOH . D 4 HOH A 16 516 69 HOH HOH . D 4 HOH A 17 517 161 HOH HOH . D 4 HOH A 18 518 188 HOH HOH . D 4 HOH A 19 519 128 HOH HOH . D 4 HOH A 20 520 33 HOH HOH . D 4 HOH A 21 521 71 HOH HOH . D 4 HOH A 22 522 106 HOH HOH . D 4 HOH A 23 523 124 HOH HOH . D 4 HOH A 24 524 150 HOH HOH . D 4 HOH A 25 525 11 HOH HOH . D 4 HOH A 26 526 56 HOH HOH . D 4 HOH A 27 527 13 HOH HOH . D 4 HOH A 28 528 25 HOH HOH . D 4 HOH A 29 529 148 HOH HOH . D 4 HOH A 30 530 20 HOH HOH . D 4 HOH A 31 531 50 HOH HOH . D 4 HOH A 32 532 172 HOH HOH . D 4 HOH A 33 533 198 HOH HOH . D 4 HOH A 34 534 70 HOH HOH . D 4 HOH A 35 535 196 HOH HOH . D 4 HOH A 36 536 171 HOH HOH . D 4 HOH A 37 537 101 HOH HOH . D 4 HOH A 38 538 231 HOH HOH . D 4 HOH A 39 539 36 HOH HOH . D 4 HOH A 40 540 40 HOH HOH . D 4 HOH A 41 541 4 HOH HOH . D 4 HOH A 42 542 30 HOH HOH . D 4 HOH A 43 543 21 HOH HOH . D 4 HOH A 44 544 14 HOH HOH . D 4 HOH A 45 545 7 HOH HOH . D 4 HOH A 46 546 23 HOH HOH . D 4 HOH A 47 547 78 HOH HOH . D 4 HOH A 48 548 38 HOH HOH . D 4 HOH A 49 549 164 HOH HOH . D 4 HOH A 50 550 29 HOH HOH . D 4 HOH A 51 551 67 HOH HOH . D 4 HOH A 52 552 225 HOH HOH . D 4 HOH A 53 553 143 HOH HOH . D 4 HOH A 54 554 191 HOH HOH . D 4 HOH A 55 555 156 HOH HOH . D 4 HOH A 56 556 37 HOH HOH . D 4 HOH A 57 557 221 HOH HOH . D 4 HOH A 58 558 19 HOH HOH . D 4 HOH A 59 559 185 HOH HOH . D 4 HOH A 60 560 73 HOH HOH . D 4 HOH A 61 561 149 HOH HOH . D 4 HOH A 62 562 245 HOH HOH . D 4 HOH A 63 563 141 HOH HOH . D 4 HOH A 64 564 180 HOH HOH . D 4 HOH A 65 565 130 HOH HOH . D 4 HOH A 66 566 53 HOH HOH . D 4 HOH A 67 567 62 HOH HOH . D 4 HOH A 68 568 154 HOH HOH . D 4 HOH A 69 569 28 HOH HOH . D 4 HOH A 70 570 82 HOH HOH . D 4 HOH A 71 571 216 HOH HOH . D 4 HOH A 72 572 65 HOH HOH . D 4 HOH A 73 573 102 HOH HOH . D 4 HOH A 74 574 74 HOH HOH . D 4 HOH A 75 575 108 HOH HOH . D 4 HOH A 76 576 39 HOH HOH . D 4 HOH A 77 577 42 HOH HOH . D 4 HOH A 78 578 118 HOH HOH . D 4 HOH A 79 579 55 HOH HOH . D 4 HOH A 80 580 145 HOH HOH . D 4 HOH A 81 581 132 HOH HOH . D 4 HOH A 82 582 95 HOH HOH . D 4 HOH A 83 583 255 HOH HOH . D 4 HOH A 84 584 10 HOH HOH . D 4 HOH A 85 585 153 HOH HOH . D 4 HOH A 86 586 129 HOH HOH . D 4 HOH A 87 587 165 HOH HOH . D 4 HOH A 88 588 125 HOH HOH . D 4 HOH A 89 589 105 HOH HOH . D 4 HOH A 90 590 16 HOH HOH . D 4 HOH A 91 591 192 HOH HOH . D 4 HOH A 92 592 201 HOH HOH . D 4 HOH A 93 593 166 HOH HOH . D 4 HOH A 94 594 58 HOH HOH . D 4 HOH A 95 595 210 HOH HOH . D 4 HOH A 96 596 49 HOH HOH . D 4 HOH A 97 597 162 HOH HOH . D 4 HOH A 98 598 122 HOH HOH . D 4 HOH A 99 599 127 HOH HOH . D 4 HOH A 100 600 22 HOH HOH . D 4 HOH A 101 601 134 HOH HOH . D 4 HOH A 102 602 174 HOH HOH . D 4 HOH A 103 603 45 HOH HOH . D 4 HOH A 104 604 76 HOH HOH . D 4 HOH A 105 605 77 HOH HOH . D 4 HOH A 106 606 160 HOH HOH . D 4 HOH A 107 607 238 HOH HOH . D 4 HOH A 108 608 3 HOH HOH . D 4 HOH A 109 609 182 HOH HOH . D 4 HOH A 110 610 167 HOH HOH . D 4 HOH A 111 611 88 HOH HOH . D 4 HOH A 112 612 63 HOH HOH . D 4 HOH A 113 613 96 HOH HOH . D 4 HOH A 114 614 152 HOH HOH . D 4 HOH A 115 615 34 HOH HOH . D 4 HOH A 116 616 103 HOH HOH . D 4 HOH A 117 617 181 HOH HOH . D 4 HOH A 118 618 220 HOH HOH . D 4 HOH A 119 619 93 HOH HOH . D 4 HOH A 120 620 242 HOH HOH . D 4 HOH A 121 621 94 HOH HOH . D 4 HOH A 122 622 138 HOH HOH . D 4 HOH A 123 623 32 HOH HOH . D 4 HOH A 124 624 5 HOH HOH . D 4 HOH A 125 625 61 HOH HOH . D 4 HOH A 126 626 72 HOH HOH . D 4 HOH A 127 627 57 HOH HOH . D 4 HOH A 128 628 116 HOH HOH . D 4 HOH A 129 629 123 HOH HOH . D 4 HOH A 130 630 31 HOH HOH . D 4 HOH A 131 631 80 HOH HOH . D 4 HOH A 132 632 83 HOH HOH . D 4 HOH A 133 633 126 HOH HOH . D 4 HOH A 134 634 85 HOH HOH . D 4 HOH A 135 635 47 HOH HOH . D 4 HOH A 136 636 87 HOH HOH . D 4 HOH A 137 637 79 HOH HOH . D 4 HOH A 138 638 147 HOH HOH . D 4 HOH A 139 639 54 HOH HOH . D 4 HOH A 140 640 157 HOH HOH . D 4 HOH A 141 641 121 HOH HOH . D 4 HOH A 142 642 46 HOH HOH . D 4 HOH A 143 643 249 HOH HOH . D 4 HOH A 144 644 107 HOH HOH . D 4 HOH A 145 645 75 HOH HOH . D 4 HOH A 146 646 114 HOH HOH . D 4 HOH A 147 647 81 HOH HOH . D 4 HOH A 148 648 66 HOH HOH . D 4 HOH A 149 649 52 HOH HOH . D 4 HOH A 150 650 232 HOH HOH . D 4 HOH A 151 651 15 HOH HOH . D 4 HOH A 152 652 18 HOH HOH . D 4 HOH A 153 653 120 HOH HOH . D 4 HOH A 154 654 48 HOH HOH . D 4 HOH A 155 655 113 HOH HOH . D 4 HOH A 156 656 142 HOH HOH . D 4 HOH A 157 657 27 HOH HOH . D 4 HOH A 158 658 170 HOH HOH . D 4 HOH A 159 659 195 HOH HOH . D 4 HOH A 160 660 136 HOH HOH . D 4 HOH A 161 661 84 HOH HOH . D 4 HOH A 162 662 235 HOH HOH . D 4 HOH A 163 663 111 HOH HOH . D 4 HOH A 164 664 24 HOH HOH . D 4 HOH A 165 665 60 HOH HOH . D 4 HOH A 166 666 59 HOH HOH . D 4 HOH A 167 667 248 HOH HOH . D 4 HOH A 168 668 230 HOH HOH . D 4 HOH A 169 669 146 HOH HOH . D 4 HOH A 170 670 253 HOH HOH . D 4 HOH A 171 671 137 HOH HOH . D 4 HOH A 172 672 211 HOH HOH . D 4 HOH A 173 673 159 HOH HOH . D 4 HOH A 174 674 8 HOH HOH . D 4 HOH A 175 675 51 HOH HOH . D 4 HOH A 176 676 117 HOH HOH . D 4 HOH A 177 677 139 HOH HOH . D 4 HOH A 178 678 250 HOH HOH . D 4 HOH A 179 679 6 HOH HOH . D 4 HOH A 180 680 241 HOH HOH . D 4 HOH A 181 681 206 HOH HOH . D 4 HOH A 182 682 222 HOH HOH . D 4 HOH A 183 683 214 HOH HOH . D 4 HOH A 184 684 90 HOH HOH . D 4 HOH A 185 685 194 HOH HOH . D 4 HOH A 186 686 104 HOH HOH . D 4 HOH A 187 687 173 HOH HOH . D 4 HOH A 188 688 175 HOH HOH . D 4 HOH A 189 689 169 HOH HOH . D 4 HOH A 190 690 240 HOH HOH . D 4 HOH A 191 691 203 HOH HOH . D 4 HOH A 192 692 189 HOH HOH . D 4 HOH A 193 693 179 HOH HOH . D 4 HOH A 194 694 228 HOH HOH . D 4 HOH A 195 695 100 HOH HOH . D 4 HOH A 196 696 224 HOH HOH . D 4 HOH A 197 697 205 HOH HOH . D 4 HOH A 198 698 184 HOH HOH . D 4 HOH A 199 699 186 HOH HOH . D 4 HOH A 200 700 244 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 GPP . . . C 3 41.371 -11.995 0.425 1 23.61 ? C1 GPP 402 A 1 HETATM 2 O O1 GPP . . . C 3 42.248 -12.282 1.511 1 22.61 ? O1 GPP 402 A 1 HETATM 3 C C2 GPP . . . C 3 40.972 -13.275 -0.291 1 23.84 ? C2 GPP 402 A 1 HETATM 4 C C3 GPP . . . C 3 41.089 -13.517 -1.62 1 24.17 ? C3 GPP 402 A 1 HETATM 5 C C4 GPP . . . C 3 41.675 -12.52 -2.581 1 23.58 ? C4 GPP 402 A 1 HETATM 6 C C5 GPP . . . C 3 40.657 -14.839 -2.233 1 25.3 ? C5 GPP 402 A 1 HETATM 7 C C6 GPP . . . C 3 39.572 -15.558 -1.445 1 25.97 ? C6 GPP 402 A 1 HETATM 8 C C7 GPP . . . C 3 39.21 -16.837 -2.173 1 26.15 ? C7 GPP 402 A 1 HETATM 9 C C8 GPP . . . C 3 38.03 -17.473 -2.07 1 26.86 ? C8 GPP 402 A 1 HETATM 10 C C9 GPP . . . C 3 37.816 -18.726 -2.865 1 27.27 ? C9 GPP 402 A 1 HETATM 11 C C10 GPP . . . C 3 36.905 -17.003 -1.196 1 27.57 ? C10 GPP 402 A 1 HETATM 12 P PA GPP . . . C 3 42.323 -11.346 2.831 1 21.85 ? PA GPP 402 A 1 HETATM 13 O O1A GPP . . . C 3 40.95 -11.013 3.34 1 19.72 ? O1A GPP 402 A 1 HETATM 14 O O2A GPP . . . C 3 43.271 -12.102 3.715 1 21.75 ? O2A GPP 402 A 1 HETATM 15 O O3A GPP . . . C 3 43.041 -10.033 2.242 1 22.9 ? O3A GPP 402 A 1 HETATM 16 P PB GPP . . . C 3 43.008 -8.526 2.825 1 23.66 ? PB GPP 402 A 1 HETATM 17 O O1B GPP . . . C 3 42.908 -7.72 1.562 1 26.56 ? O1B GPP 402 A 1 HETATM 18 O O2B GPP . . . C 3 44.374 -8.442 3.49 1 26.36 ? O2B GPP 402 A 1 HETATM 19 O O3B GPP . . . C 3 41.845 -8.354 3.77 1 22.94 ? O3B GPP 402 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 19 #