data_6PZ3 # _model_server_result.job_id S1mPHM_DGUZzJ4NBk_mhOw _model_server_result.datetime_utc '2024-11-22 10:34:44' _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 6pz3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":504}' # _entry.id 6PZ3 # _exptl.entry_id 6PZ3 _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 6PZ3 _cell.length_a 98.221 _cell.length_b 98.221 _cell.length_c 81.348 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PZ3 _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 C O3' DT 3 T DT 3 1_555 C P CAR 4 T CAR 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.612 ? covale ? covale2 C O3' CAR 4 T CAR 4 1_555 C P DA 5 T DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.592 ? metalc ? metalc1 A OD1 ASP 16 A ASP 13 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? metalc ? metalc2 A OD2 ASP 16 A ASP 13 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc3 A O MET 17 A MET 14 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc4 A OD1 ASP 118 A ASP 115 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc5 A OD2 ASP 118 A ASP 115 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc6 A OE2 GLU 119 A GLU 116 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.891 ? metalc ? metalc7 D O1A XG4 . A XG4 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc8 D O1B XG4 . A XG4 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc9 D O1G XG4 . A XG4 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc10 D O1A XG4 . A XG4 501 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc11 F MG MG . A MG 503 1_555 H O HOH . A HOH 615 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc12 F MG MG . A MG 503 1_555 B O3' DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? hydrog WATSON-CRICK hydrog1 B N1 DA 1 P DA 1 1_555 C N3 DT 12 T DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 DA 1 P DA 1 1_555 C O4 DT 12 T DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N1 DG 2 P DG 2 1_555 C N3 DC 11 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N2 DG 2 P DG 2 1_555 C O2 DC 11 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O6 DG 2 P DG 2 1_555 C N4 DC 11 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DC 3 P DC 3 1_555 C N1 DG 10 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N4 DC 3 P DC 3 1_555 C O6 DG 10 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O2 DC 3 P DC 3 1_555 C N2 DG 10 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 DA 4 P DA 4 1_555 C N3 DT 9 T DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N6 DA 4 P DA 4 1_555 C O4 DT 9 T DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N3 DC 5 P DC 5 1_555 C N1 DG 8 T DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N4 DC 5 P DC 5 1_555 C O6 DG 8 T DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O2 DC 5 P DC 5 1_555 C N2 DG 8 T DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N3 DT 6 P DT 6 1_555 C N1 DA 7 T DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O4 DT 6 P DT 6 1_555 C N6 DA 7 T DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N1 DG 7 P DG 7 1_555 C N3 DC 6 T DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N2 DG 7 P DG 7 1_555 C O2 DC 6 T DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O6 DG 7 P DG 7 1_555 C N4 DC 6 T DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 DT 8 P DT 8 1_555 C N1 DA 5 T DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O4 DT 8 P DT 8 1_555 C N6 DA 5 T DA 5 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 314 n n C1 C2 GOL sing 315 n n C1 H11 GOL sing 316 n n C1 H12 GOL sing 317 n n O1 HO1 GOL sing 318 n n C2 O2 GOL sing 319 n n C2 C3 GOL sing 320 n n C2 H2 GOL sing 321 n n O2 HO2 GOL sing 322 n n C3 O3 GOL sing 323 n n C3 H31 GOL sing 324 n n C3 H32 GOL sing 325 n n O3 HO3 GOL sing 326 n n # _atom_sites.entry_id 6PZ3 _atom_sites.fract_transf_matrix[1][1] 0.010181 _atom_sites.fract_transf_matrix[1][2] 0.005878 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011756 _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] 0.012293 _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 XG4 A 1 501 433 XG4 XG4 . E 5 MG A 1 502 434 MG MG . F 5 MG A 1 503 435 MG MG . G 6 GOL A 1 504 436 GOL GOL . H 7 HOH A 1 601 83 HOH HOH . H 7 HOH A 2 602 60 HOH HOH . H 7 HOH A 3 603 97 HOH HOH . H 7 HOH A 4 604 67 HOH HOH . H 7 HOH A 5 605 1 HOH HOH . H 7 HOH A 6 606 10 HOH HOH . H 7 HOH A 7 607 54 HOH HOH . H 7 HOH A 8 608 75 HOH HOH . H 7 HOH A 9 609 18 HOH HOH . H 7 HOH A 10 610 7 HOH HOH . H 7 HOH A 11 611 80 HOH HOH . H 7 HOH A 12 612 64 HOH HOH . H 7 HOH A 13 613 56 HOH HOH . H 7 HOH A 14 614 88 HOH HOH . H 7 HOH A 15 615 102 HOH HOH . H 7 HOH A 16 616 106 HOH HOH . H 7 HOH A 17 617 36 HOH HOH . H 7 HOH A 18 618 40 HOH HOH . H 7 HOH A 19 619 48 HOH HOH . H 7 HOH A 20 620 68 HOH HOH . H 7 HOH A 21 621 17 HOH HOH . H 7 HOH A 22 622 66 HOH HOH . H 7 HOH A 23 623 5 HOH HOH . H 7 HOH A 24 624 47 HOH HOH . H 7 HOH A 25 625 57 HOH HOH . H 7 HOH A 26 626 9 HOH HOH . H 7 HOH A 27 627 53 HOH HOH . H 7 HOH A 28 628 63 HOH HOH . H 7 HOH A 29 629 101 HOH HOH . H 7 HOH A 30 630 91 HOH HOH . H 7 HOH A 31 631 31 HOH HOH . H 7 HOH A 32 632 59 HOH HOH . H 7 HOH A 33 633 22 HOH HOH . H 7 HOH A 34 634 124 HOH HOH . H 7 HOH A 35 635 51 HOH HOH . H 7 HOH A 36 636 76 HOH HOH . H 7 HOH A 37 637 37 HOH HOH . H 7 HOH A 38 638 23 HOH HOH . H 7 HOH A 39 639 72 HOH HOH . H 7 HOH A 40 640 44 HOH HOH . H 7 HOH A 41 641 61 HOH HOH . H 7 HOH A 42 642 42 HOH HOH . H 7 HOH A 43 643 52 HOH HOH . H 7 HOH A 44 644 12 HOH HOH . H 7 HOH A 45 645 93 HOH HOH . H 7 HOH A 46 646 28 HOH HOH . H 7 HOH A 47 647 84 HOH HOH . H 7 HOH A 48 648 58 HOH HOH . H 7 HOH A 49 649 94 HOH HOH . H 7 HOH A 50 650 39 HOH HOH . H 7 HOH A 51 651 13 HOH HOH . H 7 HOH A 52 652 43 HOH HOH . H 7 HOH A 53 653 55 HOH HOH . H 7 HOH A 54 654 99 HOH HOH . H 7 HOH A 55 655 41 HOH HOH . H 7 HOH A 56 656 32 HOH HOH . H 7 HOH A 57 657 89 HOH HOH . H 7 HOH A 58 658 11 HOH HOH . H 7 HOH A 59 659 121 HOH HOH . H 7 HOH A 60 660 15 HOH HOH . H 7 HOH A 61 661 21 HOH HOH . H 7 HOH A 62 662 3 HOH HOH . H 7 HOH A 63 663 98 HOH HOH . H 7 HOH A 64 664 49 HOH HOH . H 7 HOH A 65 665 27 HOH HOH . H 7 HOH A 66 666 62 HOH HOH . H 7 HOH A 67 667 100 HOH HOH . H 7 HOH A 68 668 45 HOH HOH . H 7 HOH A 69 669 71 HOH HOH . H 7 HOH A 70 670 34 HOH HOH . H 7 HOH A 71 671 2 HOH HOH . H 7 HOH A 72 672 4 HOH HOH . H 7 HOH A 73 673 16 HOH HOH . H 7 HOH A 74 674 30 HOH HOH . H 7 HOH A 75 675 46 HOH HOH . H 7 HOH A 76 676 6 HOH HOH . H 7 HOH A 77 677 38 HOH HOH . H 7 HOH A 78 678 8 HOH HOH . H 7 HOH A 79 679 109 HOH HOH . H 7 HOH A 80 680 105 HOH HOH . H 7 HOH A 81 681 14 HOH HOH . H 7 HOH A 82 682 114 HOH HOH . H 7 HOH A 83 683 74 HOH HOH . H 7 HOH A 84 684 33 HOH HOH . H 7 HOH A 85 685 85 HOH HOH . H 7 HOH A 86 686 112 HOH HOH . H 7 HOH A 87 687 103 HOH HOH . H 7 HOH A 88 688 25 HOH HOH . H 7 HOH A 89 689 65 HOH HOH . H 7 HOH A 90 690 92 HOH HOH . H 7 HOH A 91 691 108 HOH HOH . H 7 HOH A 92 692 96 HOH HOH . H 7 HOH A 93 693 87 HOH HOH . H 7 HOH A 94 694 35 HOH HOH . H 7 HOH A 95 695 123 HOH HOH . H 7 HOH A 96 696 110 HOH HOH . H 7 HOH A 97 697 90 HOH HOH . H 7 HOH A 98 698 19 HOH HOH . H 7 HOH A 99 699 77 HOH HOH . I 7 HOH P 1 101 70 HOH HOH . I 7 HOH P 2 102 104 HOH HOH . I 7 HOH P 3 103 24 HOH HOH . I 7 HOH P 4 104 20 HOH HOH . I 7 HOH P 5 105 95 HOH HOH . I 7 HOH P 6 106 78 HOH HOH . I 7 HOH P 7 107 119 HOH HOH . I 7 HOH P 8 108 82 HOH HOH . J 7 HOH T 1 101 69 HOH HOH . J 7 HOH T 2 102 50 HOH HOH . J 7 HOH T 3 103 29 HOH HOH . J 7 HOH T 4 104 79 HOH HOH . J 7 HOH T 5 105 81 HOH HOH . J 7 HOH T 6 106 73 HOH HOH . J 7 HOH T 7 107 113 HOH HOH . J 7 HOH T 8 108 86 HOH HOH . J 7 HOH T 9 109 118 HOH HOH . J 7 HOH T 10 110 125 HOH HOH . J 7 HOH T 11 111 26 HOH HOH . J 7 HOH T 12 112 111 HOH HOH . J 7 HOH T 13 113 120 HOH HOH . J 7 HOH T 14 114 117 HOH HOH . J 7 HOH T 15 115 116 HOH HOH . J 7 HOH T 16 116 115 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 -51.295 39.567 1.944 1 30.19 ? C1 GOL 504 A 1 HETATM 2 O O1 GOL . . . G 6 -50.634 38.318 1.671 1 26.07 ? O1 GOL 504 A 1 HETATM 3 C C2 GOL . . . G 6 -51.124 39.93 3.425 1 29.84 ? C2 GOL 504 A 1 HETATM 4 O O2 GOL . . . G 6 -50.054 40.834 3.572 1 22.63 ? O2 GOL 504 A 1 HETATM 5 C C3 GOL . . . G 6 -52.41 40.493 4.036 1 30.22 ? C3 GOL 504 A 1 HETATM 6 O O3 GOL . . . G 6 -52.262 40.649 5.45 1 31.02 ? O3 GOL 504 A 1 HETATM 7 H H11 GOL . . . G 6 -52.355 39.483 1.706 1 36.13 ? H11 GOL 504 A 1 HETATM 8 H H12 GOL . . . G 6 -50.868 40.353 1.322 1 36.13 ? H12 GOL 504 A 1 HETATM 9 H HO1 GOL . . . G 6 -50.801 38.058 0.741 1 31.19 ? HO1 GOL 504 A 1 HETATM 10 H H2 GOL . . . G 6 -50.882 39.012 3.961 1 35.7 ? H2 GOL 504 A 1 HETATM 11 H HO2 GOL . . . G 6 -50.278 41.68 3.13 1 27.06 ? HO2 GOL 504 A 1 HETATM 12 H H31 GOL . . . G 6 -53.24 39.818 3.827 1 36.16 ? H31 GOL 504 A 1 HETATM 13 H H32 GOL . . . G 6 -52.638 41.458 3.583 1 36.16 ? H32 GOL 504 A 1 HETATM 14 H HO3 GOL . . . G 6 -52.916 41.3 5.777 1 37.12 ? HO3 GOL 504 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #