data_5F9L # _model_server_result.job_id SIWWhe7RGMXQ5HGTt0CGWQ _model_server_result.datetime_utc '2024-11-24 15:50:00' _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 5f9l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":504}' # _entry.id 5F9L # _exptl.entry_id 5F9L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 5F9L _cell.length_a 99.111 _cell.length_b 99.111 _cell.length_c 81.856 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5F9L _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _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 _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 6 _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 covale ? covale1 B O3' DT 3 T DT 3 1_555 B P GNE 4 T GNE 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.614 ? covale ? covale2 B O3' GNE 4 T GNE 4 1_555 B P DA 5 T DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? metalc ? metalc1 A OD2 ASP 16 A ASP 13 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc2 A OD1 ASP 16 A ASP 13 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc3 A O MET 17 A MET 14 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc4 A OD2 ASP 118 A ASP 115 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc5 A OD1 ASP 118 A ASP 115 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc6 A OE2 GLU 119 A GLU 116 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc7 D O2A DZ4 . A DZ4 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc8 D O2B DZ4 . A DZ4 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc9 D O3G DZ4 . A DZ4 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc10 D O2A DZ4 . A DZ4 501 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc11 F MG MG . A MG 503 1_555 C O3' DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.877 ? hydrog WATSON-CRICK hydrog1 B N1 DA 5 T DA 5 1_555 C N3 DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 DA 5 T DA 5 1_555 C O4 DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog3 B N3 DT 6 T DT 6 1_555 C N1 DA 7 P DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DG 7 T DG 7 1_555 C N3 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N2 DG 7 T DG 7 1_555 C O2 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O6 DG 7 T DG 7 1_555 C N4 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N1 DA 8 T DA 8 1_555 C N3 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N6 DA 8 T DA 8 1_555 C O4 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 DC 9 T DC 9 1_555 C N1 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N4 DC 9 T DC 9 1_555 C O6 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O2 DC 9 T DC 9 1_555 C N2 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 DG 10 T DG 10 1_555 C N3 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N2 DG 10 T DG 10 1_555 C O2 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O6 DG 10 T DG 10 1_555 C N4 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N3 DC 11 T DC 11 1_555 C N1 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N4 DC 11 T DC 11 1_555 C O6 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B O2 DC 11 T DC 11 1_555 C N2 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N3 DT 12 T DT 12 1_555 C N1 DA 1 P DA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B O4 DT 12 T DT 12 1_555 C N6 DA 1 P DA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 369 n n C1 C2 GOL sing 370 n n C1 H11 GOL sing 371 n n C1 H12 GOL sing 372 n n O1 HO1 GOL sing 373 n n C2 O2 GOL sing 374 n n C2 C3 GOL sing 375 n n C2 H2 GOL sing 376 n n O2 HO2 GOL sing 377 n n C3 O3 GOL sing 378 n n C3 H31 GOL sing 379 n n C3 H32 GOL sing 380 n n O3 HO3 GOL sing 381 n n # _atom_sites.entry_id 5F9L _atom_sites.fract_transf_matrix[1][1] 0.01009 _atom_sites.fract_transf_matrix[1][2] 0.005825 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011651 _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] 0.012217 _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 DZ4 A 1 501 1 DZ4 DZ4 . E 5 MG A 1 502 1 MG MG . F 5 MG A 1 503 2 MG MG . G 6 GOL A 1 504 1 GOL GOL . H 7 HOH A 1 601 138 HOH HOH . H 7 HOH A 2 602 157 HOH HOH . H 7 HOH A 3 603 139 HOH HOH . H 7 HOH A 4 604 128 HOH HOH . H 7 HOH A 5 605 84 HOH HOH . H 7 HOH A 6 606 3 HOH HOH . H 7 HOH A 7 607 106 HOH HOH . H 7 HOH A 8 608 41 HOH HOH . H 7 HOH A 9 609 140 HOH HOH . H 7 HOH A 10 610 66 HOH HOH . H 7 HOH A 11 611 85 HOH HOH . H 7 HOH A 12 612 22 HOH HOH . H 7 HOH A 13 613 31 HOH HOH . H 7 HOH A 14 614 42 HOH HOH . H 7 HOH A 15 615 149 HOH HOH . H 7 HOH A 16 616 52 HOH HOH . H 7 HOH A 17 617 121 HOH HOH . H 7 HOH A 18 618 8 HOH HOH . H 7 HOH A 19 619 88 HOH HOH . H 7 HOH A 20 620 26 HOH HOH . H 7 HOH A 21 621 6 HOH HOH . H 7 HOH A 22 622 39 HOH HOH . H 7 HOH A 23 623 23 HOH HOH . H 7 HOH A 24 624 11 HOH HOH . H 7 HOH A 25 625 61 HOH HOH . H 7 HOH A 26 626 38 HOH HOH . H 7 HOH A 27 627 150 HOH HOH . H 7 HOH A 28 628 110 HOH HOH . H 7 HOH A 29 629 19 HOH HOH . H 7 HOH A 30 630 7 HOH HOH . H 7 HOH A 31 631 126 HOH HOH . H 7 HOH A 32 632 1 HOH HOH . H 7 HOH A 33 633 65 HOH HOH . H 7 HOH A 34 634 160 HOH HOH . H 7 HOH A 35 635 4 HOH HOH . H 7 HOH A 36 636 87 HOH HOH . H 7 HOH A 37 637 111 HOH HOH . H 7 HOH A 38 638 101 HOH HOH . H 7 HOH A 39 639 64 HOH HOH . H 7 HOH A 40 640 14 HOH HOH . H 7 HOH A 41 641 76 HOH HOH . H 7 HOH A 42 642 119 HOH HOH . H 7 HOH A 43 643 120 HOH HOH . H 7 HOH A 44 644 40 HOH HOH . H 7 HOH A 45 645 21 HOH HOH . H 7 HOH A 46 646 127 HOH HOH . H 7 HOH A 47 647 12 HOH HOH . H 7 HOH A 48 648 102 HOH HOH . H 7 HOH A 49 649 36 HOH HOH . H 7 HOH A 50 650 142 HOH HOH . H 7 HOH A 51 651 51 HOH HOH . H 7 HOH A 52 652 100 HOH HOH . H 7 HOH A 53 653 2 HOH HOH . H 7 HOH A 54 654 158 HOH HOH . H 7 HOH A 55 655 32 HOH HOH . H 7 HOH A 56 656 18 HOH HOH . H 7 HOH A 57 657 97 HOH HOH . H 7 HOH A 58 658 10 HOH HOH . H 7 HOH A 59 659 98 HOH HOH . H 7 HOH A 60 660 34 HOH HOH . H 7 HOH A 61 661 99 HOH HOH . H 7 HOH A 62 662 67 HOH HOH . H 7 HOH A 63 663 154 HOH HOH . H 7 HOH A 64 664 144 HOH HOH . H 7 HOH A 65 665 20 HOH HOH . H 7 HOH A 66 666 28 HOH HOH . H 7 HOH A 67 667 82 HOH HOH . H 7 HOH A 68 668 151 HOH HOH . H 7 HOH A 69 669 5 HOH HOH . H 7 HOH A 70 670 78 HOH HOH . H 7 HOH A 71 671 55 HOH HOH . H 7 HOH A 72 672 9 HOH HOH . H 7 HOH A 73 673 79 HOH HOH . H 7 HOH A 74 674 152 HOH HOH . H 7 HOH A 75 675 24 HOH HOH . H 7 HOH A 76 676 27 HOH HOH . H 7 HOH A 77 677 16 HOH HOH . H 7 HOH A 78 678 89 HOH HOH . H 7 HOH A 79 679 68 HOH HOH . H 7 HOH A 80 680 53 HOH HOH . H 7 HOH A 81 681 147 HOH HOH . H 7 HOH A 82 682 130 HOH HOH . H 7 HOH A 83 683 129 HOH HOH . H 7 HOH A 84 684 118 HOH HOH . H 7 HOH A 85 685 92 HOH HOH . H 7 HOH A 86 686 77 HOH HOH . H 7 HOH A 87 687 137 HOH HOH . H 7 HOH A 88 688 117 HOH HOH . H 7 HOH A 89 689 103 HOH HOH . H 7 HOH A 90 690 44 HOH HOH . H 7 HOH A 91 691 47 HOH HOH . H 7 HOH A 92 692 115 HOH HOH . H 7 HOH A 93 693 159 HOH HOH . H 7 HOH A 94 694 49 HOH HOH . H 7 HOH A 95 695 107 HOH HOH . H 7 HOH A 96 696 123 HOH HOH . H 7 HOH A 97 697 116 HOH HOH . H 7 HOH A 98 698 134 HOH HOH . H 7 HOH A 99 699 25 HOH HOH . H 7 HOH A 100 700 93 HOH HOH . H 7 HOH A 101 701 50 HOH HOH . H 7 HOH A 102 702 30 HOH HOH . H 7 HOH A 103 703 58 HOH HOH . H 7 HOH A 104 704 54 HOH HOH . H 7 HOH A 105 705 104 HOH HOH . H 7 HOH A 106 706 91 HOH HOH . H 7 HOH A 107 707 156 HOH HOH . H 7 HOH A 108 708 15 HOH HOH . H 7 HOH A 109 709 145 HOH HOH . H 7 HOH A 110 710 46 HOH HOH . H 7 HOH A 111 711 109 HOH HOH . H 7 HOH A 112 712 105 HOH HOH . H 7 HOH A 113 713 122 HOH HOH . H 7 HOH A 114 714 56 HOH HOH . H 7 HOH A 115 715 136 HOH HOH . H 7 HOH A 116 716 112 HOH HOH . H 7 HOH A 117 717 131 HOH HOH . H 7 HOH A 118 718 13 HOH HOH . H 7 HOH A 119 719 17 HOH HOH . H 7 HOH A 120 720 57 HOH HOH . H 7 HOH A 121 721 62 HOH HOH . H 7 HOH A 122 722 33 HOH HOH . H 7 HOH A 123 723 164 HOH HOH . H 7 HOH A 124 724 153 HOH HOH . H 7 HOH A 125 725 135 HOH HOH . H 7 HOH A 126 726 86 HOH HOH . H 7 HOH A 127 727 125 HOH HOH . H 7 HOH A 128 728 94 HOH HOH . H 7 HOH A 129 729 90 HOH HOH . H 7 HOH A 130 730 141 HOH HOH . H 7 HOH A 131 731 163 HOH HOH . H 7 HOH A 132 732 59 HOH HOH . H 7 HOH A 133 733 48 HOH HOH . H 7 HOH A 134 734 114 HOH HOH . H 7 HOH A 135 735 81 HOH HOH . H 7 HOH A 136 736 37 HOH HOH . H 7 HOH A 137 737 155 HOH HOH . H 7 HOH A 138 738 45 HOH HOH . H 7 HOH A 139 739 108 HOH HOH . H 7 HOH A 140 740 63 HOH HOH . H 7 HOH A 141 741 60 HOH HOH . H 7 HOH A 142 742 43 HOH HOH . H 7 HOH A 143 743 161 HOH HOH . H 7 HOH A 144 744 146 HOH HOH . H 7 HOH A 145 745 29 HOH HOH . H 7 HOH A 146 746 132 HOH HOH . H 7 HOH A 147 747 96 HOH HOH . H 7 HOH A 148 748 83 HOH HOH . H 7 HOH A 149 749 95 HOH HOH . H 7 HOH A 150 750 35 HOH HOH . I 7 HOH T 1 101 72 HOH HOH . I 7 HOH T 2 102 73 HOH HOH . I 7 HOH T 3 103 71 HOH HOH . I 7 HOH T 4 104 80 HOH HOH . I 7 HOH T 5 105 70 HOH HOH . I 7 HOH T 6 106 148 HOH HOH . I 7 HOH T 7 107 133 HOH HOH . I 7 HOH T 8 108 75 HOH HOH . I 7 HOH T 9 109 143 HOH HOH . J 7 HOH P 1 101 162 HOH HOH . J 7 HOH P 2 102 113 HOH HOH . J 7 HOH P 3 103 69 HOH HOH . J 7 HOH P 4 104 124 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 . . . G 6 52.131 -40.054 -13.938 1 28.11 ? C1 GOL 504 A 1 HETATM 2 O O1 GOL . . . G 6 51.085 -39.113 -14.036 1 29.4 ? O1 GOL 504 A 1 HETATM 3 C C2 GOL . . . G 6 51.948 -40.918 -12.693 1 29.72 ? C2 GOL 504 A 1 HETATM 4 O O2 GOL . . . G 6 50.576 -41.052 -12.389 1 29.38 ? O2 GOL 504 A 1 HETATM 5 C C3 GOL . . . G 6 52.678 -40.282 -11.515 1 26.35 ? C3 GOL 504 A 1 HETATM 6 O O3 GOL . . . G 6 52.697 -41.18 -10.427 1 27.17 ? O3 GOL 504 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #