data_5YVB # _model_server_result.job_id 6vMlfym0MuS9qaoDexFAwA _model_server_result.datetime_utc '2024-11-23 12:57:49' _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 5yvb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":504}' # _entry.id 5YVB # _exptl.entry_id 5YVB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 4 _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 90 _cell.entry_id 5YVB _cell.length_a 66.777 _cell.length_b 77.547 _cell.length_c 84.478 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YVB _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 ? 3 C N N ? 3 D N N ? 3 E N N ? 3 F 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 covale ? covale1 A C MET 246 A MET 396 1_555 A N CAS 247 A CAS 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C CAS 247 A CAS 397 1_555 A N LEU 248 A LEU 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _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 180 n n C1 C2 GOL sing 181 n n C1 H11 GOL sing 182 n n C1 H12 GOL sing 183 n n O1 HO1 GOL sing 184 n n C2 O2 GOL sing 185 n n C2 C3 GOL sing 186 n n C2 H2 GOL sing 187 n n O2 HO2 GOL sing 188 n n C3 O3 GOL sing 189 n n C3 H31 GOL sing 190 n n C3 H32 GOL sing 191 n n O3 HO3 GOL sing 192 n n # _atom_sites.entry_id 5YVB _atom_sites.fract_transf_matrix[1][1] 0.014975 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012895 _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] 0.011837 _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 92C A 1 501 501 92C C11 . C 3 GOL A 1 502 601 GOL GOL . D 3 GOL A 1 503 602 GOL GOL . E 3 GOL A 1 504 603 GOL GOL . F 3 GOL A 1 505 604 GOL GOL . G 4 PGE A 1 506 605 PGE PGE . H 5 CL A 1 507 701 CL CL . I 6 HOH A 1 601 99 HOH HOH . I 6 HOH A 2 602 77 HOH HOH . I 6 HOH A 3 603 18 HOH HOH . I 6 HOH A 4 604 151 HOH HOH . I 6 HOH A 5 605 134 HOH HOH . I 6 HOH A 6 606 221 HOH HOH . I 6 HOH A 7 607 184 HOH HOH . I 6 HOH A 8 608 14 HOH HOH . I 6 HOH A 9 609 174 HOH HOH . I 6 HOH A 10 610 58 HOH HOH . I 6 HOH A 11 611 81 HOH HOH . I 6 HOH A 12 612 114 HOH HOH . I 6 HOH A 13 613 164 HOH HOH . I 6 HOH A 14 614 86 HOH HOH . I 6 HOH A 15 615 40 HOH HOH . I 6 HOH A 16 616 132 HOH HOH . I 6 HOH A 17 617 168 HOH HOH . I 6 HOH A 18 618 6 HOH HOH . I 6 HOH A 19 619 34 HOH HOH . I 6 HOH A 20 620 124 HOH HOH . I 6 HOH A 21 621 74 HOH HOH . I 6 HOH A 22 622 195 HOH HOH . I 6 HOH A 23 623 12 HOH HOH . I 6 HOH A 24 624 198 HOH HOH . I 6 HOH A 25 625 112 HOH HOH . I 6 HOH A 26 626 75 HOH HOH . I 6 HOH A 27 627 1 HOH HOH . I 6 HOH A 28 628 11 HOH HOH . I 6 HOH A 29 629 51 HOH HOH . I 6 HOH A 30 630 147 HOH HOH . I 6 HOH A 31 631 71 HOH HOH . I 6 HOH A 32 632 35 HOH HOH . I 6 HOH A 33 633 191 HOH HOH . I 6 HOH A 34 634 155 HOH HOH . I 6 HOH A 35 635 156 HOH HOH . I 6 HOH A 36 636 22 HOH HOH . I 6 HOH A 37 637 60 HOH HOH . I 6 HOH A 38 638 220 HOH HOH . I 6 HOH A 39 639 15 HOH HOH . I 6 HOH A 40 640 49 HOH HOH . I 6 HOH A 41 641 113 HOH HOH . I 6 HOH A 42 642 153 HOH HOH . I 6 HOH A 43 643 201 HOH HOH . I 6 HOH A 44 644 50 HOH HOH . I 6 HOH A 45 645 29 HOH HOH . I 6 HOH A 46 646 103 HOH HOH . I 6 HOH A 47 647 17 HOH HOH . I 6 HOH A 48 648 185 HOH HOH . I 6 HOH A 49 649 100 HOH HOH . I 6 HOH A 50 650 24 HOH HOH . I 6 HOH A 51 651 88 HOH HOH . I 6 HOH A 52 652 37 HOH HOH . I 6 HOH A 53 653 4 HOH HOH . I 6 HOH A 54 654 3 HOH HOH . I 6 HOH A 55 655 123 HOH HOH . I 6 HOH A 56 656 10 HOH HOH . I 6 HOH A 57 657 30 HOH HOH . I 6 HOH A 58 658 42 HOH HOH . I 6 HOH A 59 659 109 HOH HOH . I 6 HOH A 60 660 9 HOH HOH . I 6 HOH A 61 661 160 HOH HOH . I 6 HOH A 62 662 154 HOH HOH . I 6 HOH A 63 663 102 HOH HOH . I 6 HOH A 64 664 158 HOH HOH . I 6 HOH A 65 665 62 HOH HOH . I 6 HOH A 66 666 32 HOH HOH . I 6 HOH A 67 667 39 HOH HOH . I 6 HOH A 68 668 44 HOH HOH . I 6 HOH A 69 669 67 HOH HOH . I 6 HOH A 70 670 152 HOH HOH . I 6 HOH A 71 671 33 HOH HOH . I 6 HOH A 72 672 83 HOH HOH . I 6 HOH A 73 673 95 HOH HOH . I 6 HOH A 74 674 157 HOH HOH . I 6 HOH A 75 675 122 HOH HOH . I 6 HOH A 76 676 72 HOH HOH . I 6 HOH A 77 677 90 HOH HOH . I 6 HOH A 78 678 78 HOH HOH . I 6 HOH A 79 679 76 HOH HOH . I 6 HOH A 80 680 59 HOH HOH . I 6 HOH A 81 681 53 HOH HOH . I 6 HOH A 82 682 79 HOH HOH . I 6 HOH A 83 683 66 HOH HOH . I 6 HOH A 84 684 96 HOH HOH . I 6 HOH A 85 685 115 HOH HOH . I 6 HOH A 86 686 54 HOH HOH . I 6 HOH A 87 687 31 HOH HOH . I 6 HOH A 88 688 150 HOH HOH . I 6 HOH A 89 689 25 HOH HOH . I 6 HOH A 90 690 48 HOH HOH . I 6 HOH A 91 691 57 HOH HOH . I 6 HOH A 92 692 91 HOH HOH . I 6 HOH A 93 693 127 HOH HOH . I 6 HOH A 94 694 45 HOH HOH . I 6 HOH A 95 695 116 HOH HOH . I 6 HOH A 96 696 8 HOH HOH . I 6 HOH A 97 697 107 HOH HOH . I 6 HOH A 98 698 181 HOH HOH . I 6 HOH A 99 699 2 HOH HOH . I 6 HOH A 100 700 56 HOH HOH . I 6 HOH A 101 701 189 HOH HOH . I 6 HOH A 102 702 186 HOH HOH . I 6 HOH A 103 703 21 HOH HOH . I 6 HOH A 104 704 111 HOH HOH . I 6 HOH A 105 705 7 HOH HOH . I 6 HOH A 106 706 188 HOH HOH . I 6 HOH A 107 707 38 HOH HOH . I 6 HOH A 108 708 196 HOH HOH . I 6 HOH A 109 709 171 HOH HOH . I 6 HOH A 110 710 105 HOH HOH . I 6 HOH A 111 711 26 HOH HOH . I 6 HOH A 112 712 65 HOH HOH . I 6 HOH A 113 713 36 HOH HOH . I 6 HOH A 114 714 68 HOH HOH . I 6 HOH A 115 715 87 HOH HOH . I 6 HOH A 116 716 183 HOH HOH . I 6 HOH A 117 717 20 HOH HOH . I 6 HOH A 118 718 110 HOH HOH . I 6 HOH A 119 719 193 HOH HOH . I 6 HOH A 120 720 16 HOH HOH . I 6 HOH A 121 721 190 HOH HOH . I 6 HOH A 122 722 130 HOH HOH . I 6 HOH A 123 723 106 HOH HOH . I 6 HOH A 124 724 97 HOH HOH . I 6 HOH A 125 725 133 HOH HOH . I 6 HOH A 126 726 140 HOH HOH . I 6 HOH A 127 727 43 HOH HOH . I 6 HOH A 128 728 176 HOH HOH . I 6 HOH A 129 729 118 HOH HOH . I 6 HOH A 130 730 55 HOH HOH . I 6 HOH A 131 731 145 HOH HOH . I 6 HOH A 132 732 172 HOH HOH . I 6 HOH A 133 733 101 HOH HOH . I 6 HOH A 134 734 23 HOH HOH . I 6 HOH A 135 735 179 HOH HOH . I 6 HOH A 136 736 73 HOH HOH . I 6 HOH A 137 737 80 HOH HOH . I 6 HOH A 138 738 19 HOH HOH . I 6 HOH A 139 739 169 HOH HOH . I 6 HOH A 140 740 148 HOH HOH . I 6 HOH A 141 741 120 HOH HOH . I 6 HOH A 142 742 159 HOH HOH . I 6 HOH A 143 743 192 HOH HOH . I 6 HOH A 144 744 70 HOH HOH . I 6 HOH A 145 745 163 HOH HOH . I 6 HOH A 146 746 187 HOH HOH . I 6 HOH A 147 747 177 HOH HOH . I 6 HOH A 148 748 178 HOH HOH . I 6 HOH A 149 749 63 HOH HOH . I 6 HOH A 150 750 117 HOH HOH . I 6 HOH A 151 751 108 HOH HOH . I 6 HOH A 152 752 89 HOH HOH . I 6 HOH A 153 753 135 HOH HOH . I 6 HOH A 154 754 98 HOH HOH . I 6 HOH A 155 755 119 HOH HOH . I 6 HOH A 156 756 166 HOH HOH . I 6 HOH A 157 757 128 HOH HOH . I 6 HOH A 158 758 165 HOH HOH . I 6 HOH A 159 759 142 HOH HOH . I 6 HOH A 160 760 92 HOH HOH . I 6 HOH A 161 761 27 HOH HOH . I 6 HOH A 162 762 197 HOH HOH . I 6 HOH A 163 763 200 HOH HOH . I 6 HOH A 164 764 136 HOH HOH . I 6 HOH A 165 765 182 HOH HOH . I 6 HOH A 166 766 69 HOH HOH . I 6 HOH A 167 767 13 HOH HOH . I 6 HOH A 168 768 203 HOH HOH . I 6 HOH A 169 769 194 HOH HOH . I 6 HOH A 170 770 217 HOH HOH . I 6 HOH A 171 771 162 HOH HOH . I 6 HOH A 172 772 144 HOH HOH . I 6 HOH A 173 773 93 HOH HOH . I 6 HOH A 174 774 207 HOH HOH . I 6 HOH A 175 775 222 HOH HOH . I 6 HOH A 176 776 46 HOH HOH . I 6 HOH A 177 777 167 HOH HOH . I 6 HOH A 178 778 216 HOH HOH . I 6 HOH A 179 779 199 HOH HOH . I 6 HOH A 180 780 175 HOH HOH . I 6 HOH A 181 781 204 HOH HOH . I 6 HOH A 182 782 212 HOH HOH . I 6 HOH A 183 783 209 HOH HOH . I 6 HOH A 184 784 214 HOH HOH . I 6 HOH A 185 785 137 HOH HOH . I 6 HOH A 186 786 215 HOH HOH . I 6 HOH A 187 787 205 HOH HOH . I 6 HOH A 188 788 202 HOH HOH . I 6 HOH A 189 789 61 HOH HOH . I 6 HOH A 190 790 121 HOH HOH . I 6 HOH A 191 791 94 HOH HOH . I 6 HOH A 192 792 52 HOH HOH . I 6 HOH A 193 793 126 HOH HOH . I 6 HOH A 194 794 131 HOH HOH . I 6 HOH A 195 795 85 HOH HOH . I 6 HOH A 196 796 143 HOH HOH . I 6 HOH A 197 797 141 HOH HOH . I 6 HOH A 198 798 84 HOH HOH . I 6 HOH A 199 799 129 HOH HOH . I 6 HOH A 200 800 41 HOH HOH . I 6 HOH A 201 801 210 HOH HOH . I 6 HOH A 202 802 206 HOH HOH . I 6 HOH A 203 803 211 HOH HOH . I 6 HOH A 204 804 64 HOH HOH . I 6 HOH A 205 805 28 HOH HOH . I 6 HOH A 206 806 104 HOH HOH . I 6 HOH A 207 807 149 HOH HOH . I 6 HOH A 208 808 208 HOH HOH . I 6 HOH A 209 809 82 HOH HOH . I 6 HOH A 210 810 146 HOH HOH . I 6 HOH A 211 811 47 HOH HOH . I 6 HOH A 212 812 218 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 . . . E 3 -9.667 2.611 -12.086 1 88 ? C1 GOL 504 A 1 HETATM 2 O O1 GOL . . . E 3 -11.051 2.451 -12.004 1 86.38 ? O1 GOL 504 A 1 HETATM 3 C C2 GOL . . . E 3 -9.024 1.654 -11.034 1 87.87 ? C2 GOL 504 A 1 HETATM 4 O O2 GOL . . . E 3 -7.673 1.933 -10.813 1 89 ? O2 GOL 504 A 1 HETATM 5 C C3 GOL . . . E 3 -9.884 1.81 -9.75 1 81.87 ? C3 GOL 504 A 1 HETATM 6 O O3 GOL . . . E 3 -9.165 1.219 -8.702 1 73.76 ? O3 GOL 504 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 6 #