data_8RYZ # _model_server_result.job_id 8mK2r_ZyUMnaAhzxkauNSw _model_server_result.datetime_utc '2024-11-23 08:39:47' _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 8ryz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":507}' # _entry.id 8RYZ # _exptl.entry_id 8RYZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 5 _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 120 _cell.entry_id 8RYZ _cell.length_a 118.002 _cell.length_b 118.002 _cell.length_c 72.803 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RYZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 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,E,F,G,H,I,J,K _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 ? 5 F N N ? 5 G N N ? 5 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 O TYR 53 A TYR 53 1_555 I NA NA . A NA 508 2_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc2 A NE2 HIS 71 A HIS 71 1_555 B NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc3 A NE2 HIS 167 A HIS 167 1_555 B NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc4 A NE2 HIS 171 A HIS 171 1_555 B NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc5 A O PHE 339 A PHE 339 1_555 I NA NA . A NA 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc6 B NI NI . A NI 501 1_555 C NAT AVJ . A AVJ 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc7 B NI NI . A NI 501 1_555 D N3 IMD . A IMD 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc8 B NI NI . A NI 501 1_555 E N3 IMD . A IMD 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc9 I NA NA . A NA 508 1_555 J O2 NHE . A NHE 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.892 ? metalc ? metalc10 I NA NA . A NA 508 1_555 J O3 NHE . A NHE 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.948 ? metalc ? metalc11 I NA NA . A NA 508 1_555 K O HOH . A HOH 659 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? metalc ? metalc12 I NA NA . A NA 508 1_555 K O HOH . A HOH 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? # _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 159 n n C1 C2 GOL sing 160 n n C1 H11 GOL sing 161 n n C1 H12 GOL sing 162 n n O1 HO1 GOL sing 163 n n C2 O2 GOL sing 164 n n C2 C3 GOL sing 165 n n C2 H2 GOL sing 166 n n O2 HO2 GOL sing 167 n n C3 O3 GOL sing 168 n n C3 H31 GOL sing 169 n n C3 H32 GOL sing 170 n n O3 HO3 GOL sing 171 n n # _atom_sites.entry_id 8RYZ _atom_sites.fract_transf_matrix[1][1] 0.008474 _atom_sites.fract_transf_matrix[1][2] 0.004893 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009785 _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] 0.013736 _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 NI A 1 501 1 NI NI . C 3 AVJ A 1 502 1 AVJ AVJ . D 4 IMD A 1 503 1 IMD IMD . E 4 IMD A 1 504 2 IMD IMD . F 5 GOL A 1 505 2 GOL GOL . G 5 GOL A 1 506 4 GOL GOL . H 5 GOL A 1 507 5 GOL GOL . I 6 NA A 1 508 1 NA NA . J 7 NHE A 1 509 1 NHE NHE . K 8 HOH A 1 601 458 HOH HOH . K 8 HOH A 2 602 474 HOH HOH . K 8 HOH A 3 603 468 HOH HOH . K 8 HOH A 4 604 494 HOH HOH . K 8 HOH A 5 605 499 HOH HOH . K 8 HOH A 6 606 460 HOH HOH . K 8 HOH A 7 607 445 HOH HOH . K 8 HOH A 8 608 488 HOH HOH . K 8 HOH A 9 609 479 HOH HOH . K 8 HOH A 10 610 136 HOH HOH . K 8 HOH A 11 611 463 HOH HOH . K 8 HOH A 12 612 453 HOH HOH . K 8 HOH A 13 613 495 HOH HOH . K 8 HOH A 14 614 71 HOH HOH . K 8 HOH A 15 615 101 HOH HOH . K 8 HOH A 16 616 485 HOH HOH . K 8 HOH A 17 617 3 HOH HOH . K 8 HOH A 18 618 137 HOH HOH . K 8 HOH A 19 619 103 HOH HOH . K 8 HOH A 20 620 117 HOH HOH . K 8 HOH A 21 621 13 HOH HOH . K 8 HOH A 22 622 493 HOH HOH . K 8 HOH A 23 623 116 HOH HOH . K 8 HOH A 24 624 169 HOH HOH . K 8 HOH A 25 625 500 HOH HOH . K 8 HOH A 26 626 19 HOH HOH . K 8 HOH A 27 627 96 HOH HOH . K 8 HOH A 28 628 118 HOH HOH . K 8 HOH A 29 629 15 HOH HOH . K 8 HOH A 30 630 457 HOH HOH . K 8 HOH A 31 631 51 HOH HOH . K 8 HOH A 32 632 91 HOH HOH . K 8 HOH A 33 633 459 HOH HOH . K 8 HOH A 34 634 145 HOH HOH . K 8 HOH A 35 635 35 HOH HOH . K 8 HOH A 36 636 8 HOH HOH . K 8 HOH A 37 637 1 HOH HOH . K 8 HOH A 38 638 108 HOH HOH . K 8 HOH A 39 639 50 HOH HOH . K 8 HOH A 40 640 37 HOH HOH . K 8 HOH A 41 641 418 HOH HOH . K 8 HOH A 42 642 43 HOH HOH . K 8 HOH A 43 643 100 HOH HOH . K 8 HOH A 44 644 12 HOH HOH . K 8 HOH A 45 645 482 HOH HOH . K 8 HOH A 46 646 33 HOH HOH . K 8 HOH A 47 647 10 HOH HOH . K 8 HOH A 48 648 36 HOH HOH . K 8 HOH A 49 649 187 HOH HOH . K 8 HOH A 50 650 26 HOH HOH . K 8 HOH A 51 651 112 HOH HOH . K 8 HOH A 52 652 209 HOH HOH . K 8 HOH A 53 653 149 HOH HOH . K 8 HOH A 54 654 32 HOH HOH . K 8 HOH A 55 655 491 HOH HOH . K 8 HOH A 56 656 56 HOH HOH . K 8 HOH A 57 657 5 HOH HOH . K 8 HOH A 58 658 16 HOH HOH . K 8 HOH A 59 659 64 HOH HOH . K 8 HOH A 60 660 69 HOH HOH . K 8 HOH A 61 661 80 HOH HOH . K 8 HOH A 62 662 6 HOH HOH . K 8 HOH A 63 663 17 HOH HOH . K 8 HOH A 64 664 121 HOH HOH . K 8 HOH A 65 665 122 HOH HOH . K 8 HOH A 66 666 181 HOH HOH . K 8 HOH A 67 667 38 HOH HOH . K 8 HOH A 68 668 133 HOH HOH . K 8 HOH A 69 669 25 HOH HOH . K 8 HOH A 70 670 48 HOH HOH . K 8 HOH A 71 671 89 HOH HOH . K 8 HOH A 72 672 28 HOH HOH . K 8 HOH A 73 673 120 HOH HOH . K 8 HOH A 74 674 92 HOH HOH . K 8 HOH A 75 675 7 HOH HOH . K 8 HOH A 76 676 191 HOH HOH . K 8 HOH A 77 677 47 HOH HOH . K 8 HOH A 78 678 130 HOH HOH . K 8 HOH A 79 679 206 HOH HOH . K 8 HOH A 80 680 86 HOH HOH . K 8 HOH A 81 681 29 HOH HOH . K 8 HOH A 82 682 46 HOH HOH . K 8 HOH A 83 683 119 HOH HOH . K 8 HOH A 84 684 83 HOH HOH . K 8 HOH A 85 685 143 HOH HOH . K 8 HOH A 86 686 152 HOH HOH . K 8 HOH A 87 687 39 HOH HOH . K 8 HOH A 88 688 40 HOH HOH . K 8 HOH A 89 689 52 HOH HOH . K 8 HOH A 90 690 466 HOH HOH . K 8 HOH A 91 691 72 HOH HOH . K 8 HOH A 92 692 178 HOH HOH . K 8 HOH A 93 693 114 HOH HOH . K 8 HOH A 94 694 115 HOH HOH . K 8 HOH A 95 695 4 HOH HOH . K 8 HOH A 96 696 23 HOH HOH . K 8 HOH A 97 697 2 HOH HOH . K 8 HOH A 98 698 54 HOH HOH . K 8 HOH A 99 699 53 HOH HOH . K 8 HOH A 100 700 11 HOH HOH . K 8 HOH A 101 701 20 HOH HOH . K 8 HOH A 102 702 193 HOH HOH . K 8 HOH A 103 703 93 HOH HOH . K 8 HOH A 104 704 138 HOH HOH . K 8 HOH A 105 705 146 HOH HOH . K 8 HOH A 106 706 335 HOH HOH . K 8 HOH A 107 707 190 HOH HOH . K 8 HOH A 108 708 164 HOH HOH . K 8 HOH A 109 709 63 HOH HOH . K 8 HOH A 110 710 42 HOH HOH . K 8 HOH A 111 711 27 HOH HOH . K 8 HOH A 112 712 140 HOH HOH . K 8 HOH A 113 713 22 HOH HOH . K 8 HOH A 114 714 123 HOH HOH . K 8 HOH A 115 715 443 HOH HOH . K 8 HOH A 116 716 14 HOH HOH . K 8 HOH A 117 717 144 HOH HOH . K 8 HOH A 118 718 170 HOH HOH . K 8 HOH A 119 719 85 HOH HOH . K 8 HOH A 120 720 49 HOH HOH . K 8 HOH A 121 721 67 HOH HOH . K 8 HOH A 122 722 44 HOH HOH . K 8 HOH A 123 723 99 HOH HOH . K 8 HOH A 124 724 472 HOH HOH . K 8 HOH A 125 725 220 HOH HOH . K 8 HOH A 126 726 230 HOH HOH . K 8 HOH A 127 727 109 HOH HOH . K 8 HOH A 128 728 75 HOH HOH . K 8 HOH A 129 729 441 HOH HOH . K 8 HOH A 130 730 159 HOH HOH . K 8 HOH A 131 731 90 HOH HOH . K 8 HOH A 132 732 167 HOH HOH . K 8 HOH A 133 733 88 HOH HOH . K 8 HOH A 134 734 336 HOH HOH . K 8 HOH A 135 735 41 HOH HOH . K 8 HOH A 136 736 73 HOH HOH . K 8 HOH A 137 737 78 HOH HOH . K 8 HOH A 138 738 126 HOH HOH . K 8 HOH A 139 739 18 HOH HOH . K 8 HOH A 140 740 30 HOH HOH . K 8 HOH A 141 741 59 HOH HOH . K 8 HOH A 142 742 74 HOH HOH . K 8 HOH A 143 743 106 HOH HOH . K 8 HOH A 144 744 95 HOH HOH . K 8 HOH A 145 745 471 HOH HOH . K 8 HOH A 146 746 467 HOH HOH . K 8 HOH A 147 747 450 HOH HOH . K 8 HOH A 148 748 448 HOH HOH . K 8 HOH A 149 749 201 HOH HOH . K 8 HOH A 150 750 161 HOH HOH . K 8 HOH A 151 751 433 HOH HOH . K 8 HOH A 152 752 497 HOH HOH . K 8 HOH A 153 753 24 HOH HOH . K 8 HOH A 154 754 9 HOH HOH . K 8 HOH A 155 755 141 HOH HOH . K 8 HOH A 156 756 334 HOH HOH . K 8 HOH A 157 757 62 HOH HOH . K 8 HOH A 158 758 31 HOH HOH . K 8 HOH A 159 759 142 HOH HOH . K 8 HOH A 160 760 125 HOH HOH . K 8 HOH A 161 761 452 HOH HOH . K 8 HOH A 162 762 45 HOH HOH . K 8 HOH A 163 763 464 HOH HOH . K 8 HOH A 164 764 21 HOH HOH . K 8 HOH A 165 765 57 HOH HOH . K 8 HOH A 166 766 156 HOH HOH . K 8 HOH A 167 767 333 HOH HOH . K 8 HOH A 168 768 498 HOH HOH . K 8 HOH A 169 769 102 HOH HOH . K 8 HOH A 170 770 111 HOH HOH . K 8 HOH A 171 771 61 HOH HOH . K 8 HOH A 172 772 147 HOH HOH . K 8 HOH A 173 773 377 HOH HOH . K 8 HOH A 174 774 487 HOH HOH . K 8 HOH A 175 775 454 HOH HOH . K 8 HOH A 176 776 476 HOH HOH . K 8 HOH A 177 777 79 HOH HOH . K 8 HOH A 178 778 447 HOH HOH . K 8 HOH A 179 779 60 HOH HOH . K 8 HOH A 180 780 456 HOH HOH . K 8 HOH A 181 781 34 HOH HOH . K 8 HOH A 182 782 446 HOH HOH . K 8 HOH A 183 783 465 HOH HOH . K 8 HOH A 184 784 76 HOH HOH . K 8 HOH A 185 785 134 HOH HOH . K 8 HOH A 186 786 455 HOH HOH . K 8 HOH A 187 787 470 HOH HOH . K 8 HOH A 188 788 162 HOH HOH . K 8 HOH A 189 789 478 HOH HOH . K 8 HOH A 190 790 461 HOH HOH . K 8 HOH A 191 791 66 HOH HOH . K 8 HOH A 192 792 168 HOH HOH . K 8 HOH A 193 793 379 HOH HOH . K 8 HOH A 194 794 475 HOH HOH . K 8 HOH A 195 795 58 HOH HOH . K 8 HOH A 196 796 413 HOH HOH . K 8 HOH A 197 797 68 HOH HOH . K 8 HOH A 198 798 127 HOH HOH . K 8 HOH A 199 799 203 HOH HOH . K 8 HOH A 200 800 477 HOH HOH . K 8 HOH A 201 801 419 HOH HOH . K 8 HOH A 202 802 65 HOH HOH . K 8 HOH A 203 803 55 HOH HOH . K 8 HOH A 204 804 202 HOH HOH . K 8 HOH A 205 805 132 HOH HOH . K 8 HOH A 206 806 484 HOH HOH . K 8 HOH A 207 807 469 HOH HOH . K 8 HOH A 208 808 451 HOH HOH . K 8 HOH A 209 809 481 HOH HOH . K 8 HOH A 210 810 77 HOH HOH . K 8 HOH A 211 811 480 HOH HOH . K 8 HOH A 212 812 444 HOH HOH . K 8 HOH A 213 813 489 HOH HOH . K 8 HOH A 214 814 356 HOH HOH . K 8 HOH A 215 815 81 HOH HOH . K 8 HOH A 216 816 70 HOH HOH . K 8 HOH A 217 817 131 HOH HOH . K 8 HOH A 218 818 87 HOH HOH . K 8 HOH A 219 819 339 HOH HOH . K 8 HOH A 220 820 337 HOH HOH . K 8 HOH A 221 821 449 HOH HOH . K 8 HOH A 222 822 212 HOH HOH . K 8 HOH A 223 823 222 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 . . . H 5 -40.953 40.227 -29.908 1 44.12 ? C1 GOL 507 A 1 HETATM 2 O O1 GOL . . . H 5 -40.791 39.936 -31.258 1 45.85 ? O1 GOL 507 A 1 HETATM 3 C C2 GOL . . . H 5 -39.715 39.725 -29.156 1 48.04 ? C2 GOL 507 A 1 HETATM 4 O O2 GOL . . . H 5 -39.826 40.1 -27.799 1 53.76 ? O2 GOL 507 A 1 HETATM 5 C C3 GOL . . . H 5 -39.473 38.214 -29.246 1 50.41 ? C3 GOL 507 A 1 HETATM 6 O O3 GOL . . . H 5 -38.92 37.716 -28.045 1 49.74 ? O3 GOL 507 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #