data_5D0R # _model_server_result.job_id s0oRRhT00xq4mFO-ocFu8w _model_server_result.datetime_utc '2024-11-19 11:35:23' _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 5d0r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":512}' # _entry.id 5D0R # _exptl.entry_id 5D0R _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 2 _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 5D0R _cell.length_a 99.403 _cell.length_b 99.403 _cell.length_c 99.978 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5D0R _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _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,E,F,G,H,I,J,K,L,M,N,O _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 ? 6 M N N ? 6 N 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 ALA 252 A ALA 252 1_555 A N CME 253 A CME 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C CME 253 A CME 253 1_555 A N THR 254 A THR 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? # _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 200 n n C1 C2 GOL sing 201 n n C1 H11 GOL sing 202 n n C1 H12 GOL sing 203 n n O1 HO1 GOL sing 204 n n C2 O2 GOL sing 205 n n C2 C3 GOL sing 206 n n C2 H2 GOL sing 207 n n O2 HO2 GOL sing 208 n n C3 O3 GOL sing 209 n n C3 H31 GOL sing 210 n n C3 H32 GOL sing 211 n n O3 HO3 GOL sing 212 n n # _atom_sites.entry_id 5D0R _atom_sites.fract_transf_matrix[1][1] 0.01006 _atom_sites.fract_transf_matrix[1][2] 0.005808 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011616 _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] 0.010002 _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 B1T A 1 501 1 B1T B1T . C 3 ACT A 1 502 1 ACT ACT . D 4 EDO A 1 503 1 EDO EDO . E 4 EDO A 1 504 2 EDO EDO . F 4 EDO A 1 505 3 EDO EDO . G 4 EDO A 1 506 4 EDO EDO . H 4 EDO A 1 507 5 EDO EDO . I 4 EDO A 1 508 7 EDO EDO . J 5 DMS A 1 509 1 DMS DMS . K 5 DMS A 1 510 2 DMS DMS . L 5 DMS A 1 511 3 DMS DMS . M 6 GOL A 1 512 1 GOL GOL . N 6 GOL A 1 513 2 GOL GOL . O 7 HOH A 1 601 145 HOH HOH . O 7 HOH A 2 602 205 HOH HOH . O 7 HOH A 3 603 89 HOH HOH . O 7 HOH A 4 604 40 HOH HOH . O 7 HOH A 5 605 43 HOH HOH . O 7 HOH A 6 606 21 HOH HOH . O 7 HOH A 7 607 77 HOH HOH . O 7 HOH A 8 608 131 HOH HOH . O 7 HOH A 9 609 133 HOH HOH . O 7 HOH A 10 610 61 HOH HOH . O 7 HOH A 11 611 31 HOH HOH . O 7 HOH A 12 612 105 HOH HOH . O 7 HOH A 13 613 115 HOH HOH . O 7 HOH A 14 614 38 HOH HOH . O 7 HOH A 15 615 121 HOH HOH . O 7 HOH A 16 616 189 HOH HOH . O 7 HOH A 17 617 114 HOH HOH . O 7 HOH A 18 618 182 HOH HOH . O 7 HOH A 19 619 13 HOH HOH . O 7 HOH A 20 620 42 HOH HOH . O 7 HOH A 21 621 25 HOH HOH . O 7 HOH A 22 622 100 HOH HOH . O 7 HOH A 23 623 112 HOH HOH . O 7 HOH A 24 624 56 HOH HOH . O 7 HOH A 25 625 73 HOH HOH . O 7 HOH A 26 626 47 HOH HOH . O 7 HOH A 27 627 161 HOH HOH . O 7 HOH A 28 628 41 HOH HOH . O 7 HOH A 29 629 144 HOH HOH . O 7 HOH A 30 630 130 HOH HOH . O 7 HOH A 31 631 96 HOH HOH . O 7 HOH A 32 632 118 HOH HOH . O 7 HOH A 33 633 18 HOH HOH . O 7 HOH A 34 634 44 HOH HOH . O 7 HOH A 35 635 178 HOH HOH . O 7 HOH A 36 636 204 HOH HOH . O 7 HOH A 37 637 119 HOH HOH . O 7 HOH A 38 638 66 HOH HOH . O 7 HOH A 39 639 1 HOH HOH . O 7 HOH A 40 640 72 HOH HOH . O 7 HOH A 41 641 85 HOH HOH . O 7 HOH A 42 642 39 HOH HOH . O 7 HOH A 43 643 81 HOH HOH . O 7 HOH A 44 644 74 HOH HOH . O 7 HOH A 45 645 34 HOH HOH . O 7 HOH A 46 646 5 HOH HOH . O 7 HOH A 47 647 50 HOH HOH . O 7 HOH A 48 648 137 HOH HOH . O 7 HOH A 49 649 4 HOH HOH . O 7 HOH A 50 650 111 HOH HOH . O 7 HOH A 51 651 210 HOH HOH . O 7 HOH A 52 652 12 HOH HOH . O 7 HOH A 53 653 16 HOH HOH . O 7 HOH A 54 654 3 HOH HOH . O 7 HOH A 55 655 179 HOH HOH . O 7 HOH A 56 656 191 HOH HOH . O 7 HOH A 57 657 69 HOH HOH . O 7 HOH A 58 658 22 HOH HOH . O 7 HOH A 59 659 23 HOH HOH . O 7 HOH A 60 660 37 HOH HOH . O 7 HOH A 61 661 206 HOH HOH . O 7 HOH A 62 662 86 HOH HOH . O 7 HOH A 63 663 175 HOH HOH . O 7 HOH A 64 664 76 HOH HOH . O 7 HOH A 65 665 15 HOH HOH . O 7 HOH A 66 666 198 HOH HOH . O 7 HOH A 67 667 17 HOH HOH . O 7 HOH A 68 668 10 HOH HOH . O 7 HOH A 69 669 60 HOH HOH . O 7 HOH A 70 670 53 HOH HOH . O 7 HOH A 71 671 217 HOH HOH . O 7 HOH A 72 672 163 HOH HOH . O 7 HOH A 73 673 102 HOH HOH . O 7 HOH A 74 674 62 HOH HOH . O 7 HOH A 75 675 64 HOH HOH . O 7 HOH A 76 676 167 HOH HOH . O 7 HOH A 77 677 168 HOH HOH . O 7 HOH A 78 678 87 HOH HOH . O 7 HOH A 79 679 19 HOH HOH . O 7 HOH A 80 680 215 HOH HOH . O 7 HOH A 81 681 88 HOH HOH . O 7 HOH A 82 682 35 HOH HOH . O 7 HOH A 83 683 36 HOH HOH . O 7 HOH A 84 684 80 HOH HOH . O 7 HOH A 85 685 54 HOH HOH . O 7 HOH A 86 686 63 HOH HOH . O 7 HOH A 87 687 221 HOH HOH . O 7 HOH A 88 688 28 HOH HOH . O 7 HOH A 89 689 48 HOH HOH . O 7 HOH A 90 690 101 HOH HOH . O 7 HOH A 91 691 2 HOH HOH . O 7 HOH A 92 692 162 HOH HOH . O 7 HOH A 93 693 83 HOH HOH . O 7 HOH A 94 694 194 HOH HOH . O 7 HOH A 95 695 173 HOH HOH . O 7 HOH A 96 696 151 HOH HOH . O 7 HOH A 97 697 14 HOH HOH . O 7 HOH A 98 698 211 HOH HOH . O 7 HOH A 99 699 149 HOH HOH . O 7 HOH A 100 700 30 HOH HOH . O 7 HOH A 101 701 65 HOH HOH . O 7 HOH A 102 702 67 HOH HOH . O 7 HOH A 103 703 113 HOH HOH . O 7 HOH A 104 704 180 HOH HOH . O 7 HOH A 105 705 146 HOH HOH . O 7 HOH A 106 706 190 HOH HOH . O 7 HOH A 107 707 108 HOH HOH . O 7 HOH A 108 708 90 HOH HOH . O 7 HOH A 109 709 11 HOH HOH . O 7 HOH A 110 710 177 HOH HOH . O 7 HOH A 111 711 174 HOH HOH . O 7 HOH A 112 712 134 HOH HOH . O 7 HOH A 113 713 127 HOH HOH . O 7 HOH A 114 714 75 HOH HOH . O 7 HOH A 115 715 8 HOH HOH . O 7 HOH A 116 716 122 HOH HOH . O 7 HOH A 117 717 91 HOH HOH . O 7 HOH A 118 718 106 HOH HOH . O 7 HOH A 119 719 6 HOH HOH . O 7 HOH A 120 720 95 HOH HOH . O 7 HOH A 121 721 192 HOH HOH . O 7 HOH A 122 722 124 HOH HOH . O 7 HOH A 123 723 45 HOH HOH . O 7 HOH A 124 724 97 HOH HOH . O 7 HOH A 125 725 132 HOH HOH . O 7 HOH A 126 726 98 HOH HOH . O 7 HOH A 127 727 201 HOH HOH . O 7 HOH A 128 728 33 HOH HOH . O 7 HOH A 129 729 9 HOH HOH . O 7 HOH A 130 730 138 HOH HOH . O 7 HOH A 131 731 55 HOH HOH . O 7 HOH A 132 732 99 HOH HOH . O 7 HOH A 133 733 176 HOH HOH . O 7 HOH A 134 734 57 HOH HOH . O 7 HOH A 135 735 196 HOH HOH . O 7 HOH A 136 736 219 HOH HOH . O 7 HOH A 137 737 84 HOH HOH . O 7 HOH A 138 738 202 HOH HOH . O 7 HOH A 139 739 183 HOH HOH . O 7 HOH A 140 740 140 HOH HOH . O 7 HOH A 141 741 165 HOH HOH . O 7 HOH A 142 742 7 HOH HOH . O 7 HOH A 143 743 152 HOH HOH . O 7 HOH A 144 744 188 HOH HOH . O 7 HOH A 145 745 58 HOH HOH . O 7 HOH A 146 746 117 HOH HOH . O 7 HOH A 147 747 32 HOH HOH . O 7 HOH A 148 748 171 HOH HOH . O 7 HOH A 149 749 71 HOH HOH . O 7 HOH A 150 750 94 HOH HOH . O 7 HOH A 151 751 203 HOH HOH . O 7 HOH A 152 752 123 HOH HOH . O 7 HOH A 153 753 150 HOH HOH . O 7 HOH A 154 754 184 HOH HOH . O 7 HOH A 155 755 51 HOH HOH . O 7 HOH A 156 756 46 HOH HOH . O 7 HOH A 157 757 93 HOH HOH . O 7 HOH A 158 758 79 HOH HOH . O 7 HOH A 159 759 78 HOH HOH . O 7 HOH A 160 760 129 HOH HOH . O 7 HOH A 161 761 20 HOH HOH . O 7 HOH A 162 762 29 HOH HOH . O 7 HOH A 163 763 216 HOH HOH . O 7 HOH A 164 764 170 HOH HOH . O 7 HOH A 165 765 185 HOH HOH . O 7 HOH A 166 766 27 HOH HOH . O 7 HOH A 167 767 200 HOH HOH . O 7 HOH A 168 768 135 HOH HOH . O 7 HOH A 169 769 70 HOH HOH . O 7 HOH A 170 770 169 HOH HOH . O 7 HOH A 171 771 59 HOH HOH . O 7 HOH A 172 772 164 HOH HOH . O 7 HOH A 173 773 197 HOH HOH . O 7 HOH A 174 774 128 HOH HOH . O 7 HOH A 175 775 187 HOH HOH . O 7 HOH A 176 776 126 HOH HOH . O 7 HOH A 177 777 199 HOH HOH . O 7 HOH A 178 778 52 HOH HOH . O 7 HOH A 179 779 139 HOH HOH . O 7 HOH A 180 780 143 HOH HOH . O 7 HOH A 181 781 109 HOH HOH . O 7 HOH A 182 782 159 HOH HOH . O 7 HOH A 183 783 141 HOH HOH . O 7 HOH A 184 784 104 HOH HOH . O 7 HOH A 185 785 68 HOH HOH . O 7 HOH A 186 786 153 HOH HOH . O 7 HOH A 187 787 147 HOH HOH . O 7 HOH A 188 788 125 HOH HOH . O 7 HOH A 189 789 186 HOH HOH . O 7 HOH A 190 790 160 HOH HOH . O 7 HOH A 191 791 213 HOH HOH . O 7 HOH A 192 792 107 HOH HOH . O 7 HOH A 193 793 103 HOH HOH . O 7 HOH A 194 794 157 HOH HOH . O 7 HOH A 195 795 218 HOH HOH . O 7 HOH A 196 796 142 HOH HOH . O 7 HOH A 197 797 156 HOH HOH . O 7 HOH A 198 798 92 HOH HOH . O 7 HOH A 199 799 136 HOH HOH . O 7 HOH A 200 800 193 HOH HOH . O 7 HOH A 201 801 181 HOH HOH . O 7 HOH A 202 802 172 HOH HOH . O 7 HOH A 203 803 214 HOH HOH . O 7 HOH A 204 804 212 HOH HOH . O 7 HOH A 205 805 155 HOH HOH . O 7 HOH A 206 806 148 HOH HOH . O 7 HOH A 207 807 154 HOH HOH . O 7 HOH A 208 808 110 HOH HOH . O 7 HOH A 209 809 207 HOH HOH . O 7 HOH A 210 810 220 HOH HOH . O 7 HOH A 211 811 209 HOH HOH . O 7 HOH A 212 812 222 HOH HOH . O 7 HOH A 213 813 116 HOH HOH . O 7 HOH A 214 814 208 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 . . . M 6 33.792 14.614 -7.667 1 42.66 ? C1 GOL 512 A 1 HETATM 2 O O1 GOL . . . M 6 33.026 15.02 -6.551 1 39.92 ? O1 GOL 512 A 1 HETATM 3 C C2 GOL . . . M 6 34.553 13.26 -7.602 1 42.5 ? C2 GOL 512 A 1 HETATM 4 O O2 GOL . . . M 6 34.052 12.269 -6.737 1 37.58 ? O2 GOL 512 A 1 HETATM 5 C C3 GOL . . . M 6 34.544 12.504 -8.939 1 46.59 ? C3 GOL 512 A 1 HETATM 6 O O3 GOL . . . M 6 35.787 12.671 -9.63 1 44.01 ? O3 GOL 512 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 427 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 6 #