data_8A7L # _model_server_result.job_id eLCXHm1G-X5VJNznQQyJRA _model_server_result.datetime_utc '2024-11-14 17:20:02' _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 8a7l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":506}' # _entry.id 8A7L # _exptl.entry_id 8A7L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 314.209 _entity.id 5 _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 8A7L _cell.length_a 86.17 _cell.length_b 86.17 _cell.length_c 119.61 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8A7L _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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,H _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' 6_555 -x,-x+y,-z+2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 79.74 # _struct_asym.details ? _struct_asym.entity_id 5 _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 OD2 ASP 96 A ASP 179 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc2 A OD1 ASP 96 A ASP 179 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc3 A OD2 ASP 100 A ASP 183 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc4 A OD2 ASP 100 A ASP 183 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc5 A OD2 ASP 236 A ASP 319 1_555 B MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc6 B MG MG . A MG 501 1_555 F O12 ZOL . A ZOL 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc7 B MG MG . A MG 501 1_555 F O15 ZOL . A ZOL 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc8 B MG MG . A MG 501 1_555 H O HOH . A HOH 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc9 B MG MG . A MG 501 1_555 H O HOH . A HOH 616 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc10 B MG MG . A MG 501 1_555 H O HOH . A HOH 692 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc11 C MG MG . A MG 502 1_555 F O16 ZOL . A ZOL 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc12 C MG MG . A MG 502 1_555 F O11 ZOL . A ZOL 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc13 C MG MG . A MG 502 1_555 H O HOH . A HOH 618 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc14 C MG MG . A MG 502 1_555 H O HOH . A HOH 737 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc15 D MG MG . A MG 503 1_555 F O16 ZOL . A ZOL 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc16 D MG MG . A MG 503 1_555 H O HOH . A HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc17 D MG MG . A MG 503 1_555 H O HOH . A HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc18 D MG MG . A MG 503 1_555 H O HOH . A HOH 693 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? # _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 142 n n C1 C2 GPP sing 143 n n C1 H11 GPP sing 144 n n C1 H12 GPP sing 145 n n O1 PA GPP sing 146 n n C2 C3 GPP doub 147 e n C2 H2 GPP sing 148 n n C3 C4 GPP sing 149 n n C3 C5 GPP sing 150 n n C4 H41 GPP sing 151 n n C4 H42 GPP sing 152 n n C4 H43 GPP sing 153 n n C5 C6 GPP sing 154 n n C5 H51 GPP sing 155 n n C5 H52 GPP sing 156 n n C6 C7 GPP sing 157 n n C6 H61 GPP sing 158 n n C6 H62 GPP sing 159 n n C7 C8 GPP doub 160 n n C7 H7 GPP sing 161 n n C8 C9 GPP sing 162 n n C8 C10 GPP sing 163 n n C9 H91 GPP sing 164 n n C9 H92 GPP sing 165 n n C9 H93 GPP sing 166 n n C10 H101 GPP sing 167 n n C10 H102 GPP sing 168 n n C10 H103 GPP sing 169 n n PA O1A GPP doub 170 n n PA O2A GPP sing 171 n n PA O3A GPP sing 172 n n O2A HOA2 GPP sing 173 n n O3A PB GPP sing 174 n n PB O1B GPP doub 175 n n PB O2B GPP sing 176 n n PB O3B GPP sing 177 n n O2B HOB2 GPP sing 178 n n O3B HOB3 GPP sing 179 n n # _atom_sites.entry_id 8A7L _atom_sites.fract_transf_matrix[1][1] 0.011605 _atom_sites.fract_transf_matrix[1][2] 0.0067 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0134 _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] 0.008361 _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 1 501 584 MG MG . C 2 MG A 1 502 585 MG MG . D 2 MG A 1 503 586 MG MG . E 3 GOL A 1 504 684 GOL GOL . F 4 ZOL A 1 505 984 ZOL ZOL . G 5 GPP A 1 506 1084 GPP GPP . H 6 HOH A 1 601 83 HOH HOH . H 6 HOH A 2 602 6 HOH HOH . H 6 HOH A 3 603 123 HOH HOH . H 6 HOH A 4 604 72 HOH HOH . H 6 HOH A 5 605 48 HOH HOH . H 6 HOH A 6 606 158 HOH HOH . H 6 HOH A 7 607 193 HOH HOH . H 6 HOH A 8 608 100 HOH HOH . H 6 HOH A 9 609 88 HOH HOH . H 6 HOH A 10 610 50 HOH HOH . H 6 HOH A 11 611 119 HOH HOH . H 6 HOH A 12 612 35 HOH HOH . H 6 HOH A 13 613 3 HOH HOH . H 6 HOH A 14 614 12 HOH HOH . H 6 HOH A 15 615 106 HOH HOH . H 6 HOH A 16 616 191 HOH HOH . H 6 HOH A 17 617 159 HOH HOH . H 6 HOH A 18 618 192 HOH HOH . H 6 HOH A 19 619 133 HOH HOH . H 6 HOH A 20 620 51 HOH HOH . H 6 HOH A 21 621 57 HOH HOH . H 6 HOH A 22 622 164 HOH HOH . H 6 HOH A 23 623 33 HOH HOH . H 6 HOH A 24 624 34 HOH HOH . H 6 HOH A 25 625 190 HOH HOH . H 6 HOH A 26 626 22 HOH HOH . H 6 HOH A 27 627 46 HOH HOH . H 6 HOH A 28 628 89 HOH HOH . H 6 HOH A 29 629 110 HOH HOH . H 6 HOH A 30 630 99 HOH HOH . H 6 HOH A 31 631 9 HOH HOH . H 6 HOH A 32 632 117 HOH HOH . H 6 HOH A 33 633 90 HOH HOH . H 6 HOH A 34 634 25 HOH HOH . H 6 HOH A 35 635 23 HOH HOH . H 6 HOH A 36 636 85 HOH HOH . H 6 HOH A 37 637 8 HOH HOH . H 6 HOH A 38 638 44 HOH HOH . H 6 HOH A 39 639 129 HOH HOH . H 6 HOH A 40 640 18 HOH HOH . H 6 HOH A 41 641 24 HOH HOH . H 6 HOH A 42 642 113 HOH HOH . H 6 HOH A 43 643 58 HOH HOH . H 6 HOH A 44 644 10 HOH HOH . H 6 HOH A 45 645 160 HOH HOH . H 6 HOH A 46 646 170 HOH HOH . H 6 HOH A 47 647 147 HOH HOH . H 6 HOH A 48 648 55 HOH HOH . H 6 HOH A 49 649 95 HOH HOH . H 6 HOH A 50 650 16 HOH HOH . H 6 HOH A 51 651 30 HOH HOH . H 6 HOH A 52 652 47 HOH HOH . H 6 HOH A 53 653 21 HOH HOH . H 6 HOH A 54 654 29 HOH HOH . H 6 HOH A 55 655 54 HOH HOH . H 6 HOH A 56 656 52 HOH HOH . H 6 HOH A 57 657 31 HOH HOH . H 6 HOH A 58 658 39 HOH HOH . H 6 HOH A 59 659 65 HOH HOH . H 6 HOH A 60 660 15 HOH HOH . H 6 HOH A 61 661 7 HOH HOH . H 6 HOH A 62 662 1 HOH HOH . H 6 HOH A 63 663 40 HOH HOH . H 6 HOH A 64 664 4 HOH HOH . H 6 HOH A 65 665 111 HOH HOH . H 6 HOH A 66 666 126 HOH HOH . H 6 HOH A 67 667 98 HOH HOH . H 6 HOH A 68 668 19 HOH HOH . H 6 HOH A 69 669 96 HOH HOH . H 6 HOH A 70 670 37 HOH HOH . H 6 HOH A 71 671 132 HOH HOH . H 6 HOH A 72 672 197 HOH HOH . H 6 HOH A 73 673 168 HOH HOH . H 6 HOH A 74 674 115 HOH HOH . H 6 HOH A 75 675 116 HOH HOH . H 6 HOH A 76 676 17 HOH HOH . H 6 HOH A 77 677 43 HOH HOH . H 6 HOH A 78 678 165 HOH HOH . H 6 HOH A 79 679 5 HOH HOH . H 6 HOH A 80 680 109 HOH HOH . H 6 HOH A 81 681 71 HOH HOH . H 6 HOH A 82 682 91 HOH HOH . H 6 HOH A 83 683 186 HOH HOH . H 6 HOH A 84 684 53 HOH HOH . H 6 HOH A 85 685 120 HOH HOH . H 6 HOH A 86 686 11 HOH HOH . H 6 HOH A 87 687 178 HOH HOH . H 6 HOH A 88 688 56 HOH HOH . H 6 HOH A 89 689 114 HOH HOH . H 6 HOH A 90 690 45 HOH HOH . H 6 HOH A 91 691 75 HOH HOH . H 6 HOH A 92 692 157 HOH HOH . H 6 HOH A 93 693 175 HOH HOH . H 6 HOH A 94 694 150 HOH HOH . H 6 HOH A 95 695 59 HOH HOH . H 6 HOH A 96 696 76 HOH HOH . H 6 HOH A 97 697 64 HOH HOH . H 6 HOH A 98 698 69 HOH HOH . H 6 HOH A 99 699 155 HOH HOH . H 6 HOH A 100 700 28 HOH HOH . H 6 HOH A 101 701 195 HOH HOH . H 6 HOH A 102 702 140 HOH HOH . H 6 HOH A 103 703 152 HOH HOH . H 6 HOH A 104 704 14 HOH HOH . H 6 HOH A 105 705 13 HOH HOH . H 6 HOH A 106 706 42 HOH HOH . H 6 HOH A 107 707 86 HOH HOH . H 6 HOH A 108 708 68 HOH HOH . H 6 HOH A 109 709 105 HOH HOH . H 6 HOH A 110 710 142 HOH HOH . H 6 HOH A 111 711 134 HOH HOH . H 6 HOH A 112 712 125 HOH HOH . H 6 HOH A 113 713 32 HOH HOH . H 6 HOH A 114 714 62 HOH HOH . H 6 HOH A 115 715 104 HOH HOH . H 6 HOH A 116 716 66 HOH HOH . H 6 HOH A 117 717 20 HOH HOH . H 6 HOH A 118 718 146 HOH HOH . H 6 HOH A 119 719 107 HOH HOH . H 6 HOH A 120 720 189 HOH HOH . H 6 HOH A 121 721 102 HOH HOH . H 6 HOH A 122 722 112 HOH HOH . H 6 HOH A 123 723 81 HOH HOH . H 6 HOH A 124 724 38 HOH HOH . H 6 HOH A 125 725 67 HOH HOH . H 6 HOH A 126 726 148 HOH HOH . H 6 HOH A 127 727 73 HOH HOH . H 6 HOH A 128 728 124 HOH HOH . H 6 HOH A 129 729 80 HOH HOH . H 6 HOH A 130 730 194 HOH HOH . H 6 HOH A 131 731 63 HOH HOH . H 6 HOH A 132 732 60 HOH HOH . H 6 HOH A 133 733 84 HOH HOH . H 6 HOH A 134 734 27 HOH HOH . H 6 HOH A 135 735 143 HOH HOH . H 6 HOH A 136 736 156 HOH HOH . H 6 HOH A 137 737 176 HOH HOH . H 6 HOH A 138 738 87 HOH HOH . H 6 HOH A 139 739 74 HOH HOH . H 6 HOH A 140 740 135 HOH HOH . H 6 HOH A 141 741 153 HOH HOH . H 6 HOH A 142 742 103 HOH HOH . H 6 HOH A 143 743 2 HOH HOH . H 6 HOH A 144 744 127 HOH HOH . H 6 HOH A 145 745 70 HOH HOH . H 6 HOH A 146 746 149 HOH HOH . H 6 HOH A 147 747 61 HOH HOH . H 6 HOH A 148 748 36 HOH HOH . H 6 HOH A 149 749 49 HOH HOH . H 6 HOH A 150 750 130 HOH HOH . H 6 HOH A 151 751 145 HOH HOH . H 6 HOH A 152 752 151 HOH HOH . H 6 HOH A 153 753 78 HOH HOH . H 6 HOH A 154 754 173 HOH HOH . H 6 HOH A 155 755 172 HOH HOH . H 6 HOH A 156 756 167 HOH HOH . H 6 HOH A 157 757 77 HOH HOH . H 6 HOH A 158 758 171 HOH HOH . H 6 HOH A 159 759 144 HOH HOH . H 6 HOH A 160 760 131 HOH HOH . H 6 HOH A 161 761 121 HOH HOH . H 6 HOH A 162 762 139 HOH HOH . H 6 HOH A 163 763 128 HOH HOH . H 6 HOH A 164 764 79 HOH HOH . H 6 HOH A 165 765 199 HOH HOH . H 6 HOH A 166 766 137 HOH HOH . H 6 HOH A 167 767 136 HOH HOH . H 6 HOH A 168 768 154 HOH HOH . H 6 HOH A 169 769 101 HOH HOH . H 6 HOH A 170 770 97 HOH HOH . H 6 HOH A 171 771 94 HOH HOH . H 6 HOH A 172 772 169 HOH HOH . H 6 HOH A 173 773 138 HOH HOH . H 6 HOH A 174 774 108 HOH HOH . H 6 HOH A 175 775 196 HOH HOH . H 6 HOH A 176 776 161 HOH HOH . H 6 HOH A 177 777 198 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 . . . G 5 -41.221 36.508 27.727 1 32.65 ? C1 GPP 506 A 1 HETATM 2 O O1 GPP . . . G 5 -40.212 35.722 28.384 1 31.45 ? O1 GPP 506 A 1 HETATM 3 C C2 GPP . . . G 5 -42.421 36.701 28.625 1 32.68 ? C2 GPP 506 A 1 HETATM 4 C C3 GPP . . . G 5 -43.705 36.594 28.289 1 34.03 ? C3 GPP 506 A 1 HETATM 5 C C4 GPP . . . G 5 -44.185 36.416 26.875 1 35.02 ? C4 GPP 506 A 1 HETATM 6 C C5 GPP . . . G 5 -44.799 36.612 29.323 1 35.68 ? C5 GPP 506 A 1 HETATM 7 C C6 GPP . . . G 5 -45.744 37.795 29.21 1 36.02 ? C6 GPP 506 A 1 HETATM 8 C C7 GPP . . . G 5 -46.801 37.804 30.274 1 37.75 ? C7 GPP 506 A 1 HETATM 9 C C8 GPP . . . G 5 -48.039 38.275 30.212 1 38.02 ? C8 GPP 506 A 1 HETATM 10 C C9 GPP . . . G 5 -48.605 38.959 28.999 1 40.36 ? C9 GPP 506 A 1 HETATM 11 C C10 GPP . . . G 5 -49.008 38.146 31.343 1 39.34 ? C10 GPP 506 A 1 HETATM 12 P PA GPP . . . G 5 -39.025 36.453 29.179 1 29.53 ? PA GPP 506 A 1 HETATM 13 O O1A GPP . . . G 5 -38.101 35.413 29.715 1 30.44 ? O1A GPP 506 A 1 HETATM 14 O O2A GPP . . . G 5 -39.633 37.463 30.097 1 28.88 ? O2A GPP 506 A 1 HETATM 15 O O3A GPP . . . G 5 -38.247 37.281 28.05 1 30.75 ? O3A GPP 506 A 1 HETATM 16 P PB GPP . . . G 5 -37.499 36.94 26.654 1 29.88 ? PB GPP 506 A 1 HETATM 17 O O1B GPP . . . G 5 -38.42 37.487 25.589 1 30.28 ? O1B GPP 506 A 1 HETATM 18 O O2B GPP . . . G 5 -37.327 35.442 26.592 1 28.98 ? O2B GPP 506 A 1 HETATM 19 O O3B GPP . . . G 5 -36.178 37.668 26.742 1 29.1 ? O3B GPP 506 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 219 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 19 #