data_6YXS # _model_server_result.job_id WUmNtp5N6_bqPMhbQYrKpg _model_server_result.datetime_utc '2024-10-10 23:26:26' _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 6yxs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":503}' # _entry.id 6YXS # _exptl.entry_id 6YXS _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 6 _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 6YXS _cell.length_a 66.41 _cell.length_b 68.82 _cell.length_c 104.8 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YXS _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 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 _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 ? 3 G N N ? 3 H 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 OD1 ASN 235 A ASN 293 1_555 B MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc2 A OD2 ASP 247 A ASP 305 1_555 B MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc3 B MG MG . A MG 501 1_555 J O HOH . A HOH 655 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc4 B MG MG . A MG 501 1_555 J O HOH . A HOH 670 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc5 B MG MG . A MG 501 1_555 J O HOH . A HOH 686 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc6 B MG MG . A MG 501 1_555 J O HOH . A HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? # _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 166 n n C1 C2 GOL sing 167 n n C1 H11 GOL sing 168 n n C1 H12 GOL sing 169 n n O1 HO1 GOL sing 170 n n C2 O2 GOL sing 171 n n C2 C3 GOL sing 172 n n C2 H2 GOL sing 173 n n O2 HO2 GOL sing 174 n n C3 O3 GOL sing 175 n n C3 H31 GOL sing 176 n n C3 H32 GOL sing 177 n n O3 HO3 GOL sing 178 n n # _atom_sites.entry_id 6YXS _atom_sites.fract_transf_matrix[1][1] 0.015058 _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] 0.014531 _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] 0.009542 _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 MG A 1 501 1 MG MG . C 3 GOL A 1 502 1 GOL GOL . D 3 GOL A 1 503 2 GOL GOL . E 3 GOL A 1 504 6 GOL GOL . F 3 GOL A 1 505 7 GOL GOL . G 3 GOL A 1 506 9 GOL GOL . H 3 GOL A 1 507 10 GOL GOL . I 4 1PE A 1 508 1 1PE 1PE . J 5 HOH A 1 601 129 HOH HOH . J 5 HOH A 2 602 168 HOH HOH . J 5 HOH A 3 603 301 HOH HOH . J 5 HOH A 4 604 289 HOH HOH . J 5 HOH A 5 605 283 HOH HOH . J 5 HOH A 6 606 302 HOH HOH . J 5 HOH A 7 607 83 HOH HOH . J 5 HOH A 8 608 52 HOH HOH . J 5 HOH A 9 609 165 HOH HOH . J 5 HOH A 10 610 275 HOH HOH . J 5 HOH A 11 611 117 HOH HOH . J 5 HOH A 12 612 259 HOH HOH . J 5 HOH A 13 613 204 HOH HOH . J 5 HOH A 14 614 203 HOH HOH . J 5 HOH A 15 615 47 HOH HOH . J 5 HOH A 16 616 108 HOH HOH . J 5 HOH A 17 617 253 HOH HOH . J 5 HOH A 18 618 23 HOH HOH . J 5 HOH A 19 619 97 HOH HOH . J 5 HOH A 20 620 82 HOH HOH . J 5 HOH A 21 621 78 HOH HOH . J 5 HOH A 22 622 223 HOH HOH . J 5 HOH A 23 623 152 HOH HOH . J 5 HOH A 24 624 124 HOH HOH . J 5 HOH A 25 625 86 HOH HOH . J 5 HOH A 26 626 49 HOH HOH . J 5 HOH A 27 627 121 HOH HOH . J 5 HOH A 28 628 45 HOH HOH . J 5 HOH A 29 629 93 HOH HOH . J 5 HOH A 30 630 24 HOH HOH . J 5 HOH A 31 631 80 HOH HOH . J 5 HOH A 32 632 4 HOH HOH . J 5 HOH A 33 633 71 HOH HOH . J 5 HOH A 34 634 62 HOH HOH . J 5 HOH A 35 635 9 HOH HOH . J 5 HOH A 36 636 294 HOH HOH . J 5 HOH A 37 637 58 HOH HOH . J 5 HOH A 38 638 267 HOH HOH . J 5 HOH A 39 639 194 HOH HOH . J 5 HOH A 40 640 184 HOH HOH . J 5 HOH A 41 641 285 HOH HOH . J 5 HOH A 42 642 295 HOH HOH . J 5 HOH A 43 643 115 HOH HOH . J 5 HOH A 44 644 5 HOH HOH . J 5 HOH A 45 645 29 HOH HOH . J 5 HOH A 46 646 81 HOH HOH . J 5 HOH A 47 647 69 HOH HOH . J 5 HOH A 48 648 63 HOH HOH . J 5 HOH A 49 649 44 HOH HOH . J 5 HOH A 50 650 299 HOH HOH . J 5 HOH A 51 651 19 HOH HOH . J 5 HOH A 52 652 79 HOH HOH . J 5 HOH A 53 653 50 HOH HOH . J 5 HOH A 54 654 169 HOH HOH . J 5 HOH A 55 655 111 HOH HOH . J 5 HOH A 56 656 164 HOH HOH . J 5 HOH A 57 657 20 HOH HOH . J 5 HOH A 58 658 54 HOH HOH . J 5 HOH A 59 659 296 HOH HOH . J 5 HOH A 60 660 118 HOH HOH . J 5 HOH A 61 661 157 HOH HOH . J 5 HOH A 62 662 284 HOH HOH . J 5 HOH A 63 663 92 HOH HOH . J 5 HOH A 64 664 87 HOH HOH . J 5 HOH A 65 665 226 HOH HOH . J 5 HOH A 66 666 298 HOH HOH . J 5 HOH A 67 667 106 HOH HOH . J 5 HOH A 68 668 234 HOH HOH . J 5 HOH A 69 669 53 HOH HOH . J 5 HOH A 70 670 13 HOH HOH . J 5 HOH A 71 671 126 HOH HOH . J 5 HOH A 72 672 233 HOH HOH . J 5 HOH A 73 673 216 HOH HOH . J 5 HOH A 74 674 297 HOH HOH . J 5 HOH A 75 675 42 HOH HOH . J 5 HOH A 76 676 31 HOH HOH . J 5 HOH A 77 677 163 HOH HOH . J 5 HOH A 78 678 197 HOH HOH . J 5 HOH A 79 679 131 HOH HOH . J 5 HOH A 80 680 205 HOH HOH . J 5 HOH A 81 681 41 HOH HOH . J 5 HOH A 82 682 16 HOH HOH . J 5 HOH A 83 683 57 HOH HOH . J 5 HOH A 84 684 11 HOH HOH . J 5 HOH A 85 685 22 HOH HOH . J 5 HOH A 86 686 12 HOH HOH . J 5 HOH A 87 687 75 HOH HOH . J 5 HOH A 88 688 15 HOH HOH . J 5 HOH A 89 689 36 HOH HOH . J 5 HOH A 90 690 236 HOH HOH . J 5 HOH A 91 691 263 HOH HOH . J 5 HOH A 92 692 14 HOH HOH . J 5 HOH A 93 693 48 HOH HOH . J 5 HOH A 94 694 18 HOH HOH . J 5 HOH A 95 695 6 HOH HOH . J 5 HOH A 96 696 43 HOH HOH . J 5 HOH A 97 697 35 HOH HOH . J 5 HOH A 98 698 51 HOH HOH . J 5 HOH A 99 699 172 HOH HOH . J 5 HOH A 100 700 38 HOH HOH . J 5 HOH A 101 701 110 HOH HOH . J 5 HOH A 102 702 74 HOH HOH . J 5 HOH A 103 703 303 HOH HOH . J 5 HOH A 104 704 46 HOH HOH . J 5 HOH A 105 705 137 HOH HOH . J 5 HOH A 106 706 55 HOH HOH . J 5 HOH A 107 707 96 HOH HOH . J 5 HOH A 108 708 150 HOH HOH . J 5 HOH A 109 709 162 HOH HOH . J 5 HOH A 110 710 254 HOH HOH . J 5 HOH A 111 711 10 HOH HOH . J 5 HOH A 112 712 67 HOH HOH . J 5 HOH A 113 713 207 HOH HOH . J 5 HOH A 114 714 7 HOH HOH . J 5 HOH A 115 715 1 HOH HOH . J 5 HOH A 116 716 85 HOH HOH . J 5 HOH A 117 717 73 HOH HOH . J 5 HOH A 118 718 120 HOH HOH . J 5 HOH A 119 719 101 HOH HOH . J 5 HOH A 120 720 217 HOH HOH . J 5 HOH A 121 721 174 HOH HOH . J 5 HOH A 122 722 151 HOH HOH . J 5 HOH A 123 723 95 HOH HOH . J 5 HOH A 124 724 300 HOH HOH . J 5 HOH A 125 725 158 HOH HOH . J 5 HOH A 126 726 26 HOH HOH . J 5 HOH A 127 727 279 HOH HOH . J 5 HOH A 128 728 66 HOH HOH . J 5 HOH A 129 729 21 HOH HOH . J 5 HOH A 130 730 61 HOH HOH . J 5 HOH A 131 731 77 HOH HOH . J 5 HOH A 132 732 304 HOH HOH . J 5 HOH A 133 733 188 HOH HOH . J 5 HOH A 134 734 125 HOH HOH . J 5 HOH A 135 735 98 HOH HOH . J 5 HOH A 136 736 30 HOH HOH . J 5 HOH A 137 737 225 HOH HOH . J 5 HOH A 138 738 65 HOH HOH . J 5 HOH A 139 739 100 HOH HOH . J 5 HOH A 140 740 199 HOH HOH . J 5 HOH A 141 741 119 HOH HOH . J 5 HOH A 142 742 290 HOH HOH . J 5 HOH A 143 743 246 HOH HOH . J 5 HOH A 144 744 235 HOH HOH . J 5 HOH A 145 745 224 HOH HOH . J 5 HOH A 146 746 99 HOH HOH . J 5 HOH A 147 747 102 HOH HOH . J 5 HOH A 148 748 8 HOH HOH . J 5 HOH A 149 749 107 HOH HOH . J 5 HOH A 150 750 123 HOH HOH . J 5 HOH A 151 751 264 HOH HOH . J 5 HOH A 152 752 144 HOH HOH . J 5 HOH A 153 753 27 HOH HOH . J 5 HOH A 154 754 25 HOH HOH . J 5 HOH A 155 755 116 HOH HOH . J 5 HOH A 156 756 34 HOH HOH . J 5 HOH A 157 757 195 HOH HOH . J 5 HOH A 158 758 276 HOH HOH . J 5 HOH A 159 759 132 HOH HOH . J 5 HOH A 160 760 231 HOH HOH . J 5 HOH A 161 761 185 HOH HOH . J 5 HOH A 162 762 146 HOH HOH . J 5 HOH A 163 763 135 HOH HOH . J 5 HOH A 164 764 218 HOH HOH . J 5 HOH A 165 765 237 HOH HOH . J 5 HOH A 166 766 170 HOH HOH . J 5 HOH A 167 767 280 HOH HOH . J 5 HOH A 168 768 186 HOH HOH . J 5 HOH A 169 769 171 HOH HOH . J 5 HOH A 170 770 187 HOH HOH . J 5 HOH A 171 771 127 HOH HOH . J 5 HOH A 172 772 3 HOH HOH . J 5 HOH A 173 773 260 HOH HOH . J 5 HOH A 174 774 252 HOH HOH . J 5 HOH A 175 775 287 HOH HOH . J 5 HOH A 176 776 154 HOH HOH . J 5 HOH A 177 777 167 HOH HOH . J 5 HOH A 178 778 269 HOH HOH . J 5 HOH A 179 779 196 HOH HOH . J 5 HOH A 180 780 255 HOH HOH . J 5 HOH A 181 781 268 HOH HOH . J 5 HOH A 182 782 239 HOH HOH . J 5 HOH A 183 783 94 HOH HOH . J 5 HOH A 184 784 166 HOH HOH . J 5 HOH A 185 785 112 HOH HOH . J 5 HOH A 186 786 293 HOH HOH . J 5 HOH A 187 787 232 HOH HOH . J 5 HOH A 188 788 28 HOH HOH . J 5 HOH A 189 789 292 HOH HOH . J 5 HOH A 190 790 277 HOH HOH . J 5 HOH A 191 791 147 HOH HOH . J 5 HOH A 192 792 104 HOH HOH . J 5 HOH A 193 793 59 HOH HOH . J 5 HOH A 194 794 88 HOH HOH . J 5 HOH A 195 795 139 HOH HOH . J 5 HOH A 196 796 215 HOH HOH . J 5 HOH A 197 797 220 HOH HOH . J 5 HOH A 198 798 198 HOH HOH . J 5 HOH A 199 799 245 HOH HOH . J 5 HOH A 200 800 222 HOH HOH . J 5 HOH A 201 801 270 HOH HOH . J 5 HOH A 202 802 113 HOH HOH . J 5 HOH A 203 803 183 HOH HOH . J 5 HOH A 204 804 114 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 . . . D 3 -27.932 -10.613 12.342 1 51.05 ? C1 GOL 503 A 1 HETATM 2 O O1 GOL . . . D 3 -28.912 -11.527 12.726 1 58.15 ? O1 GOL 503 A 1 HETATM 3 C C2 GOL . . . D 3 -27.477 -9.884 13.625 1 50.08 ? C2 GOL 503 A 1 HETATM 4 O O2 GOL . . . D 3 -26.503 -10.597 14.312 1 61.73 ? O2 GOL 503 A 1 HETATM 5 C C3 GOL . . . D 3 -26.977 -8.504 13.142 1 37.84 ? C3 GOL 503 A 1 HETATM 6 O O3 GOL . . . D 3 -26.391 -7.878 14.243 1 34.77 ? O3 GOL 503 A 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 6 #