data_5NP4 # _model_server_result.job_id EuIJ5Ovg4HGoFP7hIVYL4g _model_server_result.datetime_utc '2025-07-26 08:02:12' _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 5np4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5NP4 # _exptl.entry_id 5NP4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 2 _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 5NP4 _cell.length_a 60.239 _cell.length_b 60.239 _cell.length_c 69.574 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NP4 _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id C _struct_conn.ptnr1_label_atom_id CO _struct_conn.ptnr1_label_comp_id CNC _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CNC _struct_conn.ptnr1_auth_seq_id 502 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id N3B _struct_conn.ptnr2_label_comp_id CNC _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CNC _struct_conn.ptnr2_auth_seq_id 502 _struct_conn.ptnr2_symmetry 1_555 _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 2.219 _struct_conn.pdbx_value_order ? # _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 308 n n C1 C2 GOL sing 309 n n C1 H11 GOL sing 310 n n C1 H12 GOL sing 311 n n O1 HO1 GOL sing 312 n n C2 O2 GOL sing 313 n n C2 C3 GOL sing 314 n n C2 H2 GOL sing 315 n n O2 HO2 GOL sing 316 n n C3 O3 GOL sing 317 n n C3 H31 GOL sing 318 n n C3 H32 GOL sing 319 n n O3 HO3 GOL sing 320 n n # _atom_sites.entry_id 5NP4 _atom_sites.fract_transf_matrix[1][1] 0.016601 _atom_sites.fract_transf_matrix[1][2] 0.009584 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019169 _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] 0.014373 _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 GOL A 1 501 2 GOL GOL . C 3 CNC A 1 502 800 CNC CNC . D 4 HOH A 1 601 49 HOH HOH . D 4 HOH A 2 602 77 HOH HOH . D 4 HOH A 3 603 51 HOH HOH . D 4 HOH A 4 604 116 HOH HOH . D 4 HOH A 5 605 95 HOH HOH . D 4 HOH A 6 606 129 HOH HOH . D 4 HOH A 7 607 46 HOH HOH . D 4 HOH A 8 608 40 HOH HOH . D 4 HOH A 9 609 153 HOH HOH . D 4 HOH A 10 610 130 HOH HOH . D 4 HOH A 11 611 17 HOH HOH . D 4 HOH A 12 612 27 HOH HOH . D 4 HOH A 13 613 2 HOH HOH . D 4 HOH A 14 614 73 HOH HOH . D 4 HOH A 15 615 61 HOH HOH . D 4 HOH A 16 616 32 HOH HOH . D 4 HOH A 17 617 53 HOH HOH . D 4 HOH A 18 618 10 HOH HOH . D 4 HOH A 19 619 62 HOH HOH . D 4 HOH A 20 620 68 HOH HOH . D 4 HOH A 21 621 25 HOH HOH . D 4 HOH A 22 622 18 HOH HOH . D 4 HOH A 23 623 55 HOH HOH . D 4 HOH A 24 624 13 HOH HOH . D 4 HOH A 25 625 70 HOH HOH . D 4 HOH A 26 626 24 HOH HOH . D 4 HOH A 27 627 57 HOH HOH . D 4 HOH A 28 628 44 HOH HOH . D 4 HOH A 29 629 4 HOH HOH . D 4 HOH A 30 630 48 HOH HOH . D 4 HOH A 31 631 86 HOH HOH . D 4 HOH A 32 632 7 HOH HOH . D 4 HOH A 33 633 97 HOH HOH . D 4 HOH A 34 634 6 HOH HOH . D 4 HOH A 35 635 66 HOH HOH . D 4 HOH A 36 636 41 HOH HOH . D 4 HOH A 37 637 56 HOH HOH . D 4 HOH A 38 638 30 HOH HOH . D 4 HOH A 39 639 11 HOH HOH . D 4 HOH A 40 640 3 HOH HOH . D 4 HOH A 41 641 21 HOH HOH . D 4 HOH A 42 642 5 HOH HOH . D 4 HOH A 43 643 71 HOH HOH . D 4 HOH A 44 644 34 HOH HOH . D 4 HOH A 45 645 26 HOH HOH . D 4 HOH A 46 646 29 HOH HOH . D 4 HOH A 47 647 39 HOH HOH . D 4 HOH A 48 648 124 HOH HOH . D 4 HOH A 49 649 69 HOH HOH . D 4 HOH A 50 650 151 HOH HOH . D 4 HOH A 51 651 99 HOH HOH . D 4 HOH A 52 652 31 HOH HOH . D 4 HOH A 53 653 20 HOH HOH . D 4 HOH A 54 654 83 HOH HOH . D 4 HOH A 55 655 76 HOH HOH . D 4 HOH A 56 656 50 HOH HOH . D 4 HOH A 57 657 74 HOH HOH . D 4 HOH A 58 658 65 HOH HOH . D 4 HOH A 59 659 19 HOH HOH . D 4 HOH A 60 660 136 HOH HOH . D 4 HOH A 61 661 141 HOH HOH . D 4 HOH A 62 662 33 HOH HOH . D 4 HOH A 63 663 64 HOH HOH . D 4 HOH A 64 664 92 HOH HOH . D 4 HOH A 65 665 144 HOH HOH . D 4 HOH A 66 666 119 HOH HOH . D 4 HOH A 67 667 37 HOH HOH . D 4 HOH A 68 668 36 HOH HOH . D 4 HOH A 69 669 23 HOH HOH . D 4 HOH A 70 670 139 HOH HOH . D 4 HOH A 71 671 133 HOH HOH . D 4 HOH A 72 672 38 HOH HOH . D 4 HOH A 73 673 14 HOH HOH . D 4 HOH A 74 674 123 HOH HOH . D 4 HOH A 75 675 47 HOH HOH . D 4 HOH A 76 676 67 HOH HOH . D 4 HOH A 77 677 54 HOH HOH . D 4 HOH A 78 678 35 HOH HOH . D 4 HOH A 79 679 9 HOH HOH . D 4 HOH A 80 680 22 HOH HOH . D 4 HOH A 81 681 43 HOH HOH . D 4 HOH A 82 682 16 HOH HOH . D 4 HOH A 83 683 84 HOH HOH . D 4 HOH A 84 684 137 HOH HOH . D 4 HOH A 85 685 8 HOH HOH . D 4 HOH A 86 686 146 HOH HOH . D 4 HOH A 87 687 98 HOH HOH . D 4 HOH A 88 688 131 HOH HOH . D 4 HOH A 89 689 58 HOH HOH . D 4 HOH A 90 690 12 HOH HOH . D 4 HOH A 91 691 135 HOH HOH . D 4 HOH A 92 692 154 HOH HOH . D 4 HOH A 93 693 96 HOH HOH . D 4 HOH A 94 694 120 HOH HOH . D 4 HOH A 95 695 78 HOH HOH . D 4 HOH A 96 696 28 HOH HOH . D 4 HOH A 97 697 145 HOH HOH . D 4 HOH A 98 698 60 HOH HOH . D 4 HOH A 99 699 63 HOH HOH . D 4 HOH A 100 700 140 HOH HOH . D 4 HOH A 101 701 152 HOH HOH . D 4 HOH A 102 702 122 HOH HOH . D 4 HOH A 103 703 111 HOH HOH . D 4 HOH A 104 704 103 HOH HOH . D 4 HOH A 105 705 87 HOH HOH . D 4 HOH A 106 706 88 HOH HOH . D 4 HOH A 107 707 1 HOH HOH . D 4 HOH A 108 708 106 HOH HOH . D 4 HOH A 109 709 79 HOH HOH . D 4 HOH A 110 710 42 HOH HOH . D 4 HOH A 111 711 156 HOH HOH . D 4 HOH A 112 712 149 HOH HOH . D 4 HOH A 113 713 148 HOH HOH . D 4 HOH A 114 714 90 HOH HOH . D 4 HOH A 115 715 150 HOH HOH . D 4 HOH A 116 716 127 HOH HOH . D 4 HOH A 117 717 142 HOH HOH . D 4 HOH A 118 718 114 HOH HOH . D 4 HOH A 119 719 138 HOH HOH . D 4 HOH A 120 720 94 HOH HOH . D 4 HOH A 121 721 109 HOH HOH . D 4 HOH A 122 722 75 HOH HOH . D 4 HOH A 123 723 80 HOH HOH . D 4 HOH A 124 724 89 HOH HOH . D 4 HOH A 125 725 91 HOH HOH . D 4 HOH A 126 726 59 HOH HOH . D 4 HOH A 127 727 121 HOH HOH . D 4 HOH A 128 728 128 HOH HOH . D 4 HOH A 129 729 15 HOH HOH . D 4 HOH A 130 730 85 HOH HOH . D 4 HOH A 131 731 107 HOH HOH . D 4 HOH A 132 732 155 HOH HOH . D 4 HOH A 133 733 105 HOH HOH . D 4 HOH A 134 734 104 HOH HOH . D 4 HOH A 135 735 101 HOH HOH . D 4 HOH A 136 736 118 HOH HOH . D 4 HOH A 137 737 115 HOH HOH . D 4 HOH A 138 738 81 HOH HOH . D 4 HOH A 139 739 100 HOH HOH . D 4 HOH A 140 740 125 HOH HOH . D 4 HOH A 141 741 52 HOH HOH . D 4 HOH A 142 742 45 HOH HOH . D 4 HOH A 143 743 143 HOH HOH . D 4 HOH A 144 744 72 HOH HOH . D 4 HOH A 145 745 117 HOH HOH . D 4 HOH A 146 746 112 HOH HOH . D 4 HOH A 147 747 132 HOH HOH . D 4 HOH A 148 748 82 HOH HOH . D 4 HOH A 149 749 113 HOH HOH . D 4 HOH A 150 750 93 HOH HOH . D 4 HOH A 151 751 102 HOH HOH . D 4 HOH A 152 752 147 HOH HOH . D 4 HOH A 153 753 126 HOH HOH . D 4 HOH A 154 754 134 HOH HOH . D 4 HOH A 155 755 110 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 . . . B 2 -30.55 31.875 -0.641 1 36.66 ? C1 GOL 501 A 1 HETATM 2 O O1 GOL . . . B 2 -31.676 32.017 0.179 1 37.38 ? O1 GOL 501 A 1 HETATM 3 C C2 GOL . . . B 2 -30.964 32.443 -2.017 1 38.04 ? C2 GOL 501 A 1 HETATM 4 O O2 GOL . . . B 2 -31.006 33.817 -1.957 1 39.45 ? O2 GOL 501 A 1 HETATM 5 C C3 GOL . . . B 2 -29.93 31.919 -3.051 1 39.43 ? C3 GOL 501 A 1 HETATM 6 O O3 GOL . . . B 2 -30.305 32.443 -4.311 1 38.33 ? O3 GOL 501 A 1 HETATM 7 H H11 GOL . . . B 2 -29.774 32.352 -0.309 1 44 ? H11 GOL 501 A 1 HETATM 8 H H12 GOL . . . B 2 -30.281 30.947 -0.729 1 44 ? H12 GOL 501 A 1 HETATM 9 H HO1 GOL . . . B 2 -31.473 31.674 0.93 1 44.85 ? HO1 GOL 501 A 1 HETATM 10 H H2 GOL . . . B 2 -31.862 32.158 -2.248 1 45.64 ? H2 GOL 501 A 1 HETATM 11 H HO2 GOL . . . B 2 -30.312 34.082 -1.545 1 47.34 ? HO2 GOL 501 A 1 HETATM 12 H H31 GOL . . . B 2 -29.038 32.174 -2.769 1 47.32 ? H31 GOL 501 A 1 HETATM 13 H H32 GOL . . . B 2 -29.932 30.949 -3.047 1 47.32 ? H32 GOL 501 A 1 HETATM 14 H HO3 GOL . . . B 2 -29.653 32.3 -4.838 1 45.99 ? HO3 GOL 501 A 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #