data_9M3P # _model_server_result.job_id BG9ss1i9L1ZsWiLCGsTNQg _model_server_result.datetime_utc '2025-07-09 11:45:29' _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 9m3p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":504}' # _entry.id 9M3P # _exptl.entry_id 9M3P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 4 _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 90 _cell.entry_id 9M3P _cell.length_a 100.221 _cell.length_b 100.221 _cell.length_c 109.815 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9M3P _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 E N N ? 4 F N N ? 4 G 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 O ALA 10 A ALA 50 1_555 B K K . A K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc2 A O PHE 12 A PHE 52 1_555 B K K . A K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? metalc ? metalc3 A OD1 ASN 49 A ASN 89 1_555 B K K . A K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.713 ? metalc ? metalc4 A O TYR 363 A TYR 403 1_555 B K K . A K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? metalc ? metalc5 B K K . A K 501 1_555 H O HOH . A HOH 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? # _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 129 n n C1 C2 GOL sing 130 n n C1 H11 GOL sing 131 n n C1 H12 GOL sing 132 n n O1 HO1 GOL sing 133 n n C2 O2 GOL sing 134 n n C2 C3 GOL sing 135 n n C2 H2 GOL sing 136 n n O2 HO2 GOL sing 137 n n C3 O3 GOL sing 138 n n C3 H31 GOL sing 139 n n C3 H32 GOL sing 140 n n O3 HO3 GOL sing 141 n n # _atom_sites.entry_id 9M3P _atom_sites.fract_transf_matrix[1][1] 0.009978 _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] 0.009978 _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] 0.009106 _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 K A 1 501 501 K K . C 3 SZ6 A 1 502 601 SZ6 L0R . D 3 SZ6 A 1 503 701 SZ6 L0R . E 4 GOL A 1 504 801 GOL GOL . F 4 GOL A 1 505 901 GOL GOL . G 4 GOL A 1 506 1001 GOL GOL . H 5 HOH A 1 601 229 HOH HOH . H 5 HOH A 2 602 219 HOH HOH . H 5 HOH A 3 603 133 HOH HOH . H 5 HOH A 4 604 199 HOH HOH . H 5 HOH A 5 605 170 HOH HOH . H 5 HOH A 6 606 151 HOH HOH . H 5 HOH A 7 607 22 HOH HOH . H 5 HOH A 8 608 23 HOH HOH . H 5 HOH A 9 609 44 HOH HOH . H 5 HOH A 10 610 247 HOH HOH . H 5 HOH A 11 611 20 HOH HOH . H 5 HOH A 12 612 10 HOH HOH . H 5 HOH A 13 613 237 HOH HOH . H 5 HOH A 14 614 71 HOH HOH . H 5 HOH A 15 615 79 HOH HOH . H 5 HOH A 16 616 138 HOH HOH . H 5 HOH A 17 617 61 HOH HOH . H 5 HOH A 18 618 98 HOH HOH . H 5 HOH A 19 619 32 HOH HOH . H 5 HOH A 20 620 77 HOH HOH . H 5 HOH A 21 621 63 HOH HOH . H 5 HOH A 22 622 80 HOH HOH . H 5 HOH A 23 623 95 HOH HOH . H 5 HOH A 24 624 46 HOH HOH . H 5 HOH A 25 625 172 HOH HOH . H 5 HOH A 26 626 198 HOH HOH . H 5 HOH A 27 627 73 HOH HOH . H 5 HOH A 28 628 17 HOH HOH . H 5 HOH A 29 629 82 HOH HOH . H 5 HOH A 30 630 53 HOH HOH . H 5 HOH A 31 631 70 HOH HOH . H 5 HOH A 32 632 168 HOH HOH . H 5 HOH A 33 633 31 HOH HOH . H 5 HOH A 34 634 245 HOH HOH . H 5 HOH A 35 635 169 HOH HOH . H 5 HOH A 36 636 29 HOH HOH . H 5 HOH A 37 637 197 HOH HOH . H 5 HOH A 38 638 40 HOH HOH . H 5 HOH A 39 639 155 HOH HOH . H 5 HOH A 40 640 179 HOH HOH . H 5 HOH A 41 641 52 HOH HOH . H 5 HOH A 42 642 3 HOH HOH . H 5 HOH A 43 643 62 HOH HOH . H 5 HOH A 44 644 89 HOH HOH . H 5 HOH A 45 645 74 HOH HOH . H 5 HOH A 46 646 47 HOH HOH . H 5 HOH A 47 647 216 HOH HOH . H 5 HOH A 48 648 48 HOH HOH . H 5 HOH A 49 649 122 HOH HOH . H 5 HOH A 50 650 35 HOH HOH . H 5 HOH A 51 651 187 HOH HOH . H 5 HOH A 52 652 34 HOH HOH . H 5 HOH A 53 653 13 HOH HOH . H 5 HOH A 54 654 120 HOH HOH . H 5 HOH A 55 655 166 HOH HOH . H 5 HOH A 56 656 21 HOH HOH . H 5 HOH A 57 657 164 HOH HOH . H 5 HOH A 58 658 84 HOH HOH . H 5 HOH A 59 659 214 HOH HOH . H 5 HOH A 60 660 83 HOH HOH . H 5 HOH A 61 661 184 HOH HOH . H 5 HOH A 62 662 57 HOH HOH . H 5 HOH A 63 663 250 HOH HOH . H 5 HOH A 64 664 24 HOH HOH . H 5 HOH A 65 665 25 HOH HOH . H 5 HOH A 66 666 28 HOH HOH . H 5 HOH A 67 667 91 HOH HOH . H 5 HOH A 68 668 85 HOH HOH . H 5 HOH A 69 669 105 HOH HOH . H 5 HOH A 70 670 161 HOH HOH . H 5 HOH A 71 671 90 HOH HOH . H 5 HOH A 72 672 94 HOH HOH . H 5 HOH A 73 673 38 HOH HOH . H 5 HOH A 74 674 154 HOH HOH . H 5 HOH A 75 675 193 HOH HOH . H 5 HOH A 76 676 72 HOH HOH . H 5 HOH A 77 677 67 HOH HOH . H 5 HOH A 78 678 69 HOH HOH . H 5 HOH A 79 679 114 HOH HOH . H 5 HOH A 80 680 189 HOH HOH . H 5 HOH A 81 681 235 HOH HOH . H 5 HOH A 82 682 144 HOH HOH . H 5 HOH A 83 683 58 HOH HOH . H 5 HOH A 84 684 97 HOH HOH . H 5 HOH A 85 685 56 HOH HOH . H 5 HOH A 86 686 96 HOH HOH . H 5 HOH A 87 687 59 HOH HOH . H 5 HOH A 88 688 145 HOH HOH . H 5 HOH A 89 689 43 HOH HOH . H 5 HOH A 90 690 140 HOH HOH . H 5 HOH A 91 691 177 HOH HOH . H 5 HOH A 92 692 14 HOH HOH . H 5 HOH A 93 693 60 HOH HOH . H 5 HOH A 94 694 54 HOH HOH . H 5 HOH A 95 695 135 HOH HOH . H 5 HOH A 96 696 86 HOH HOH . H 5 HOH A 97 697 116 HOH HOH . H 5 HOH A 98 698 158 HOH HOH . H 5 HOH A 99 699 4 HOH HOH . H 5 HOH A 100 700 87 HOH HOH . H 5 HOH A 101 701 127 HOH HOH . H 5 HOH A 102 702 50 HOH HOH . H 5 HOH A 103 703 123 HOH HOH . H 5 HOH A 104 704 141 HOH HOH . H 5 HOH A 105 705 27 HOH HOH . H 5 HOH A 106 706 153 HOH HOH . H 5 HOH A 107 707 234 HOH HOH . H 5 HOH A 108 708 162 HOH HOH . H 5 HOH A 109 709 178 HOH HOH . H 5 HOH A 110 710 55 HOH HOH . H 5 HOH A 111 711 132 HOH HOH . H 5 HOH A 112 712 66 HOH HOH . H 5 HOH A 113 713 137 HOH HOH . H 5 HOH A 114 714 167 HOH HOH . H 5 HOH A 115 715 12 HOH HOH . H 5 HOH A 116 716 49 HOH HOH . H 5 HOH A 117 717 113 HOH HOH . H 5 HOH A 118 718 2 HOH HOH . H 5 HOH A 119 719 143 HOH HOH . H 5 HOH A 120 720 224 HOH HOH . H 5 HOH A 121 721 106 HOH HOH . H 5 HOH A 122 722 11 HOH HOH . H 5 HOH A 123 723 51 HOH HOH . H 5 HOH A 124 724 129 HOH HOH . H 5 HOH A 125 725 65 HOH HOH . H 5 HOH A 126 726 188 HOH HOH . H 5 HOH A 127 727 68 HOH HOH . H 5 HOH A 128 728 41 HOH HOH . H 5 HOH A 129 729 209 HOH HOH . H 5 HOH A 130 730 218 HOH HOH . H 5 HOH A 131 731 78 HOH HOH . H 5 HOH A 132 732 81 HOH HOH . H 5 HOH A 133 733 101 HOH HOH . H 5 HOH A 134 734 8 HOH HOH . H 5 HOH A 135 735 136 HOH HOH . H 5 HOH A 136 736 103 HOH HOH . H 5 HOH A 137 737 88 HOH HOH . H 5 HOH A 138 738 45 HOH HOH . H 5 HOH A 139 739 192 HOH HOH . H 5 HOH A 140 740 115 HOH HOH . H 5 HOH A 141 741 76 HOH HOH . H 5 HOH A 142 742 118 HOH HOH . H 5 HOH A 143 743 163 HOH HOH . H 5 HOH A 144 744 130 HOH HOH . H 5 HOH A 145 745 233 HOH HOH . H 5 HOH A 146 746 36 HOH HOH . H 5 HOH A 147 747 64 HOH HOH . H 5 HOH A 148 748 215 HOH HOH . H 5 HOH A 149 749 92 HOH HOH . H 5 HOH A 150 750 221 HOH HOH . H 5 HOH A 151 751 109 HOH HOH . H 5 HOH A 152 752 156 HOH HOH . H 5 HOH A 153 753 93 HOH HOH . H 5 HOH A 154 754 207 HOH HOH . H 5 HOH A 155 755 30 HOH HOH . H 5 HOH A 156 756 240 HOH HOH . H 5 HOH A 157 757 160 HOH HOH . H 5 HOH A 158 758 121 HOH HOH . H 5 HOH A 159 759 200 HOH HOH . H 5 HOH A 160 760 150 HOH HOH . H 5 HOH A 161 761 213 HOH HOH . H 5 HOH A 162 762 102 HOH HOH . H 5 HOH A 163 763 203 HOH HOH . H 5 HOH A 164 764 212 HOH HOH . H 5 HOH A 165 765 104 HOH HOH . H 5 HOH A 166 766 194 HOH HOH . H 5 HOH A 167 767 148 HOH HOH . H 5 HOH A 168 768 211 HOH HOH . H 5 HOH A 169 769 16 HOH HOH . H 5 HOH A 170 770 190 HOH HOH . H 5 HOH A 171 771 249 HOH HOH . H 5 HOH A 172 772 75 HOH HOH . H 5 HOH A 173 773 117 HOH HOH . H 5 HOH A 174 774 239 HOH HOH . H 5 HOH A 175 775 26 HOH HOH . H 5 HOH A 176 776 244 HOH HOH . H 5 HOH A 177 777 238 HOH HOH . H 5 HOH A 178 778 227 HOH HOH . H 5 HOH A 179 779 147 HOH HOH . H 5 HOH A 180 780 99 HOH HOH . H 5 HOH A 181 781 242 HOH HOH . H 5 HOH A 182 782 176 HOH HOH . H 5 HOH A 183 783 107 HOH HOH . H 5 HOH A 184 784 183 HOH HOH . H 5 HOH A 185 785 226 HOH HOH . H 5 HOH A 186 786 171 HOH HOH . H 5 HOH A 187 787 205 HOH HOH . H 5 HOH A 188 788 110 HOH HOH . H 5 HOH A 189 789 173 HOH HOH . H 5 HOH A 190 790 228 HOH HOH . H 5 HOH A 191 791 246 HOH HOH . H 5 HOH A 192 792 185 HOH HOH . H 5 HOH A 193 793 255 HOH HOH . H 5 HOH A 194 794 131 HOH HOH . H 5 HOH A 195 795 112 HOH HOH . H 5 HOH A 196 796 195 HOH HOH . H 5 HOH A 197 797 126 HOH HOH . H 5 HOH A 198 798 241 HOH HOH . H 5 HOH A 199 799 204 HOH HOH . H 5 HOH A 200 800 248 HOH HOH . H 5 HOH A 201 801 256 HOH HOH . H 5 HOH A 202 802 18 HOH HOH . H 5 HOH A 203 803 165 HOH HOH . H 5 HOH A 204 804 134 HOH HOH . H 5 HOH A 205 805 100 HOH HOH . H 5 HOH A 206 806 225 HOH HOH . H 5 HOH A 207 807 202 HOH HOH . H 5 HOH A 208 808 1 HOH HOH . H 5 HOH A 209 809 111 HOH HOH . H 5 HOH A 210 810 253 HOH HOH . H 5 HOH A 211 811 42 HOH HOH . H 5 HOH A 212 812 243 HOH HOH . H 5 HOH A 213 813 191 HOH HOH . H 5 HOH A 214 814 5 HOH HOH . H 5 HOH A 215 815 174 HOH HOH . H 5 HOH A 216 816 230 HOH HOH . H 5 HOH A 217 817 231 HOH HOH . H 5 HOH A 218 818 186 HOH HOH . H 5 HOH A 219 819 175 HOH HOH . H 5 HOH A 220 820 108 HOH HOH . H 5 HOH A 221 821 9 HOH HOH . H 5 HOH A 222 822 220 HOH HOH . H 5 HOH A 223 823 6 HOH HOH . H 5 HOH A 224 824 152 HOH HOH . H 5 HOH A 225 825 252 HOH HOH . H 5 HOH A 226 826 142 HOH HOH . H 5 HOH A 227 827 196 HOH HOH . H 5 HOH A 228 828 182 HOH HOH . H 5 HOH A 229 829 208 HOH HOH . H 5 HOH A 230 830 157 HOH HOH . H 5 HOH A 231 831 206 HOH HOH . H 5 HOH A 232 832 254 HOH HOH . H 5 HOH A 233 833 33 HOH HOH . H 5 HOH A 234 834 217 HOH HOH . H 5 HOH A 235 835 15 HOH HOH . H 5 HOH A 236 836 236 HOH HOH . H 5 HOH A 237 837 146 HOH HOH . H 5 HOH A 238 838 19 HOH HOH . H 5 HOH A 239 839 125 HOH HOH . H 5 HOH A 240 840 251 HOH HOH . H 5 HOH A 241 841 139 HOH HOH . H 5 HOH A 242 842 39 HOH HOH . H 5 HOH A 243 843 149 HOH HOH . H 5 HOH A 244 844 124 HOH HOH . H 5 HOH A 245 845 180 HOH HOH . H 5 HOH A 246 846 210 HOH HOH . H 5 HOH A 247 847 181 HOH HOH . H 5 HOH A 248 848 7 HOH HOH . H 5 HOH A 249 849 159 HOH HOH . H 5 HOH A 250 850 223 HOH HOH . H 5 HOH A 251 851 201 HOH HOH . H 5 HOH A 252 852 119 HOH HOH . H 5 HOH A 253 853 232 HOH HOH . H 5 HOH A 254 854 128 HOH HOH . H 5 HOH A 255 855 222 HOH HOH . H 5 HOH A 256 856 37 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 4 -15.022 21.6 -0.847 1 74.25 ? C1 GOL 504 A 1 HETATM 2 O O1 GOL . . . E 4 -16.309 21.326 -0.361 1 74.85 ? O1 GOL 504 A 1 HETATM 3 C C2 GOL . . . E 4 -14.764 23.144 -0.759 1 70.3 ? C2 GOL 504 A 1 HETATM 4 O O2 GOL . . . E 4 -14.105 23.624 -1.887 1 75.03 ? O2 GOL 504 A 1 HETATM 5 C C3 GOL . . . E 4 -13.92 23.354 0.528 1 54.54 ? C3 GOL 504 A 1 HETATM 6 O O3 GOL . . . E 4 -14.731 22.908 1.585 1 53.73 ? O3 GOL 504 A 1 # _model_server_stats.io_time_ms 72 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 410 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 6 #