data_8VMF # _model_server_result.job_id pM7cGzEbre-_nKJ65E-VAg _model_server_result.datetime_utc '2024-11-01 19:42:50' _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 8vmf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":505}' # _entry.id 8VMF # _exptl.entry_id 8VMF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 3 _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 8VMF _cell.length_a 82.251 _cell.length_b 82.251 _cell.length_c 280.354 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VMF _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall 'P 61 2 (x,y,z+5/12)' _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,J,K,L,M _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 7 H N N ? 7 I N N ? 7 J 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 OD1 ASN 161 A ASN 186 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc2 A OD2 ASP 175 A ASP 200 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? metalc ? metalc3 A OD1 ASP 175 A ASP 200 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.626 ? metalc ? metalc4 D MG MG . A MG 501 1_555 G O1B ADP . A ADP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? metalc ? metalc5 D MG MG . A MG 501 1_555 L O HOH . A HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.907 ? metalc ? metalc6 E MG MG . A MG 502 1_555 G O3B ADP . A ADP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc7 E MG MG . A MG 502 1_555 L O HOH . A HOH 647 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 GOL sing 176 n n C1 C2 GOL sing 177 n n C1 H11 GOL sing 178 n n C1 H12 GOL sing 179 n n O1 HO1 GOL sing 180 n n C2 O2 GOL sing 181 n n C2 C3 GOL sing 182 n n C2 H2 GOL sing 183 n n O2 HO2 GOL sing 184 n n C3 O3 GOL sing 185 n n C3 H31 GOL sing 186 n n C3 H32 GOL sing 187 n n O3 HO3 GOL sing 188 n n # _atom_sites.entry_id 8VMF _atom_sites.fract_transf_matrix[1][1] 0.012158 _atom_sites.fract_transf_matrix[1][2] 0.007019 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014039 _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] 0.003567 _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 D 4 MG A 1 501 501 MG MG . E 4 MG A 1 502 502 MG MG . F 5 AF3 A 1 503 601 AF3 AF3 . G 6 ADP A 1 504 1 ADP ADP . H 7 GOL A 1 505 1 GOL GOL . I 7 GOL A 1 506 2 GOL GOL . J 7 GOL A 1 507 3 GOL GOL . K 8 CL A 1 508 1 CL CL . L 9 HOH A 1 601 120 HOH HOH . L 9 HOH A 2 602 119 HOH HOH . L 9 HOH A 3 603 38 HOH HOH . L 9 HOH A 4 604 165 HOH HOH . L 9 HOH A 5 605 123 HOH HOH . L 9 HOH A 6 606 144 HOH HOH . L 9 HOH A 7 607 162 HOH HOH . L 9 HOH A 8 608 167 HOH HOH . L 9 HOH A 9 609 160 HOH HOH . L 9 HOH A 10 610 82 HOH HOH . L 9 HOH A 11 611 153 HOH HOH . L 9 HOH A 12 612 86 HOH HOH . L 9 HOH A 13 613 37 HOH HOH . L 9 HOH A 14 614 58 HOH HOH . L 9 HOH A 15 615 35 HOH HOH . L 9 HOH A 16 616 81 HOH HOH . L 9 HOH A 17 617 135 HOH HOH . L 9 HOH A 18 618 142 HOH HOH . L 9 HOH A 19 619 158 HOH HOH . L 9 HOH A 20 620 21 HOH HOH . L 9 HOH A 21 621 51 HOH HOH . L 9 HOH A 22 622 161 HOH HOH . L 9 HOH A 23 623 19 HOH HOH . L 9 HOH A 24 624 166 HOH HOH . L 9 HOH A 25 625 107 HOH HOH . L 9 HOH A 26 626 77 HOH HOH . L 9 HOH A 27 627 133 HOH HOH . L 9 HOH A 28 628 25 HOH HOH . L 9 HOH A 29 629 3 HOH HOH . L 9 HOH A 30 630 96 HOH HOH . L 9 HOH A 31 631 117 HOH HOH . L 9 HOH A 32 632 61 HOH HOH . L 9 HOH A 33 633 66 HOH HOH . L 9 HOH A 34 634 18 HOH HOH . L 9 HOH A 35 635 164 HOH HOH . L 9 HOH A 36 636 70 HOH HOH . L 9 HOH A 37 637 15 HOH HOH . L 9 HOH A 38 638 68 HOH HOH . L 9 HOH A 39 639 141 HOH HOH . L 9 HOH A 40 640 126 HOH HOH . L 9 HOH A 41 641 44 HOH HOH . L 9 HOH A 42 642 22 HOH HOH . L 9 HOH A 43 643 69 HOH HOH . L 9 HOH A 44 644 159 HOH HOH . L 9 HOH A 45 645 131 HOH HOH . L 9 HOH A 46 646 163 HOH HOH . L 9 HOH A 47 647 129 HOH HOH . L 9 HOH A 48 648 5 HOH HOH . L 9 HOH A 49 649 14 HOH HOH . L 9 HOH A 50 650 102 HOH HOH . L 9 HOH A 51 651 17 HOH HOH . L 9 HOH A 52 652 168 HOH HOH . L 9 HOH A 53 653 13 HOH HOH . L 9 HOH A 54 654 97 HOH HOH . L 9 HOH A 55 655 46 HOH HOH . L 9 HOH A 56 656 26 HOH HOH . L 9 HOH A 57 657 31 HOH HOH . L 9 HOH A 58 658 95 HOH HOH . L 9 HOH A 59 659 62 HOH HOH . L 9 HOH A 60 660 152 HOH HOH . L 9 HOH A 61 661 4 HOH HOH . L 9 HOH A 62 662 10 HOH HOH . L 9 HOH A 63 663 73 HOH HOH . L 9 HOH A 64 664 57 HOH HOH . L 9 HOH A 65 665 88 HOH HOH . L 9 HOH A 66 666 169 HOH HOH . L 9 HOH A 67 667 8 HOH HOH . L 9 HOH A 68 668 23 HOH HOH . L 9 HOH A 69 669 56 HOH HOH . L 9 HOH A 70 670 6 HOH HOH . L 9 HOH A 71 671 9 HOH HOH . L 9 HOH A 72 672 138 HOH HOH . L 9 HOH A 73 673 49 HOH HOH . L 9 HOH A 74 674 34 HOH HOH . L 9 HOH A 75 675 12 HOH HOH . L 9 HOH A 76 676 24 HOH HOH . L 9 HOH A 77 677 2 HOH HOH . L 9 HOH A 78 678 125 HOH HOH . L 9 HOH A 79 679 92 HOH HOH . L 9 HOH A 80 680 16 HOH HOH . L 9 HOH A 81 681 83 HOH HOH . L 9 HOH A 82 682 1 HOH HOH . L 9 HOH A 83 683 122 HOH HOH . L 9 HOH A 84 684 63 HOH HOH . L 9 HOH A 85 685 124 HOH HOH . L 9 HOH A 86 686 7 HOH HOH . L 9 HOH A 87 687 40 HOH HOH . L 9 HOH A 88 688 106 HOH HOH . L 9 HOH A 89 689 150 HOH HOH . L 9 HOH A 90 690 116 HOH HOH . L 9 HOH A 91 691 84 HOH HOH . L 9 HOH A 92 692 76 HOH HOH . L 9 HOH A 93 693 59 HOH HOH . L 9 HOH A 94 694 121 HOH HOH . L 9 HOH A 95 695 157 HOH HOH . L 9 HOH A 96 696 101 HOH HOH . L 9 HOH A 97 697 50 HOH HOH . L 9 HOH A 98 698 65 HOH HOH . L 9 HOH A 99 699 33 HOH HOH . L 9 HOH A 100 700 105 HOH HOH . L 9 HOH A 101 701 154 HOH HOH . L 9 HOH A 102 702 74 HOH HOH . L 9 HOH A 103 703 149 HOH HOH . L 9 HOH A 104 704 115 HOH HOH . L 9 HOH A 105 705 155 HOH HOH . L 9 HOH A 106 706 98 HOH HOH . L 9 HOH A 107 707 127 HOH HOH . L 9 HOH A 108 708 45 HOH HOH . L 9 HOH A 109 709 118 HOH HOH . L 9 HOH A 110 710 139 HOH HOH . L 9 HOH A 111 711 113 HOH HOH . L 9 HOH A 112 712 85 HOH HOH . L 9 HOH A 113 713 104 HOH HOH . L 9 HOH A 114 714 93 HOH HOH . L 9 HOH A 115 715 103 HOH HOH . L 9 HOH A 116 716 134 HOH HOH . L 9 HOH A 117 717 11 HOH HOH . L 9 HOH A 118 718 55 HOH HOH . L 9 HOH A 119 719 136 HOH HOH . L 9 HOH A 120 720 112 HOH HOH . L 9 HOH A 121 721 109 HOH HOH . L 9 HOH A 122 722 137 HOH HOH . M 9 HOH B 1 501 27 HOH HOH . M 9 HOH B 2 502 78 HOH HOH . M 9 HOH B 3 503 128 HOH HOH . M 9 HOH B 4 504 29 HOH HOH . M 9 HOH B 5 505 47 HOH HOH . M 9 HOH B 6 506 20 HOH HOH . M 9 HOH B 7 507 91 HOH HOH . M 9 HOH B 8 508 156 HOH HOH . M 9 HOH B 9 509 48 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 GOL . . . H 7 16.695 -53.042 2.325 1 90.08 ? C1 GOL 505 A 1 HETATM 2 O O1 GOL . . . H 7 15.87 -54.018 2.928 1 96.7 ? O1 GOL 505 A 1 HETATM 3 C C2 GOL . . . H 7 15.803 -51.844 2.056 1 83.83 ? C2 GOL 505 A 1 HETATM 4 O O2 GOL . . . H 7 15.006 -51.533 3.165 1 80.79 ? O2 GOL 505 A 1 HETATM 5 C C3 GOL . . . H 7 16.752 -50.686 1.725 1 80.41 ? C3 GOL 505 A 1 HETATM 6 O O3 GOL . . . H 7 17.674 -51.134 0.749 1 74 ? O3 GOL 505 A 1 HETATM 7 H H11 GOL . . . H 7 17.436 -52.774 2.89 1 108.09 ? H11 GOL 505 A 1 HETATM 8 H H12 GOL . . . H 7 17.09 -53.345 1.493 1 108.09 ? H12 GOL 505 A 1 HETATM 9 H HO1 GOL . . . H 7 15.196 -53.601 3.257 1 116.03 ? HO1 GOL 505 A 1 HETATM 10 H H2 GOL . . . H 7 15.208 -52.036 1.315 1 100.59 ? H2 GOL 505 A 1 HETATM 11 H HO2 GOL . . . H 7 15.528 -51.299 3.808 1 96.95 ? HO2 GOL 505 A 1 HETATM 12 H H31 GOL . . . H 7 16.222 -49.93 1.428 1 96.49 ? H31 GOL 505 A 1 HETATM 13 H H32 GOL . . . H 7 17.178 -50.394 2.545 1 96.49 ? H32 GOL 505 A 1 HETATM 14 H HO3 GOL . . . H 7 18.398 -51.324 1.14 1 88.8 ? HO3 GOL 505 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #