data_5YGY
#
_model_server_result.job_id            H61py1JNeDauaYDJD6zuEA 
_model_server_result.datetime_utc      '2024-11-08 16:52:13' 
_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          5ygy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":506}' 
#
_entry.id    5YGY 
#
_exptl.entry_id    5YGY 
_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    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            5YGY 
_cell.length_a            102.149 
_cell.length_b            102.149 
_cell.length_c            171.125 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YGY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
_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
? 3 G N N 
? 3 H N N 
? 3 I 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
disulf ? disulf1 A SG CYS 178 A CYS 155 1_555 A SG CYS 382 A CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
disulf ? disulf2 A SG CYS 240 A CYS 217 1_555 A SG CYS 405 A CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf3 A SG CYS 292 A CYS 269 1_555 A SG CYS 342 A CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
#
_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 174 n n 
C1 C2 GOL sing 175 n n 
C1 H11 GOL sing 176 n n 
C1 H12 GOL sing 177 n n 
O1 HO1 GOL sing 178 n n 
C2 O2 GOL sing 179 n n 
C2 C3 GOL sing 180 n n 
C2 H2 GOL sing 181 n n 
O2 HO2 GOL sing 182 n n 
C3 O3 GOL sing 183 n n 
C3 H31 GOL sing 184 n n 
C3 H32 GOL sing 185 n n 
O3 HO3 GOL sing 186 n n 
#
_atom_sites.entry_id                     5YGY 
_atom_sites.fract_transf_matrix[1][1]    0.00979 
_atom_sites.fract_transf_matrix[1][2]    0.005652 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011304 
_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]    0.005844 
_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 IOD A 1 501 501 IOD IOD . 
C 2 IOD A 1 502 502 IOD IOD . 
D 2 IOD A 1 503 503 IOD IOD . 
E 2 IOD A 1 504 504 IOD IOD . 
F 2 IOD A 1 505 505 IOD IOD . 
G 3 GOL A 1 506 506 GOL GOL . 
H 3 GOL A 1 507 507 GOL GOL . 
I 3 GOL A 1 508 508 GOL GOL . 
J 4 0B6 A 1 509 701 0B6 0B6 . 
K 5 HOH A 1 601 1069 HOH HOH . 
K 5 HOH A 2 602 1129 HOH HOH . 
K 5 HOH A 3 603 1121 HOH HOH . 
K 5 HOH A 4 604 1101 HOH HOH . 
K 5 HOH A 5 605 1063 HOH HOH . 
K 5 HOH A 6 606 1111 HOH HOH . 
K 5 HOH A 7 607 1070 HOH HOH . 
K 5 HOH A 8 608 1007 HOH HOH . 
K 5 HOH A 9 609 1015 HOH HOH . 
K 5 HOH A 10 610 1131 HOH HOH . 
K 5 HOH A 11 611 1006 HOH HOH . 
K 5 HOH A 12 612 1089 HOH HOH . 
K 5 HOH A 13 613 1182 HOH HOH . 
K 5 HOH A 14 614 1053 HOH HOH . 
K 5 HOH A 15 615 1080 HOH HOH . 
K 5 HOH A 16 616 1033 HOH HOH . 
K 5 HOH A 17 617 1135 HOH HOH . 
K 5 HOH A 18 618 1128 HOH HOH . 
K 5 HOH A 19 619 1052 HOH HOH . 
K 5 HOH A 20 620 1140 HOH HOH . 
K 5 HOH A 21 621 1160 HOH HOH . 
K 5 HOH A 22 622 1003 HOH HOH . 
K 5 HOH A 23 623 1145 HOH HOH . 
K 5 HOH A 24 624 1044 HOH HOH . 
K 5 HOH A 25 625 1134 HOH HOH . 
K 5 HOH A 26 626 1073 HOH HOH . 
K 5 HOH A 27 627 1079 HOH HOH . 
K 5 HOH A 28 628 1055 HOH HOH . 
K 5 HOH A 29 629 1100 HOH HOH . 
K 5 HOH A 30 630 1097 HOH HOH . 
K 5 HOH A 31 631 1019 HOH HOH . 
K 5 HOH A 32 632 1028 HOH HOH . 
K 5 HOH A 33 633 1064 HOH HOH . 
K 5 HOH A 34 634 1014 HOH HOH . 
K 5 HOH A 35 635 1031 HOH HOH . 
K 5 HOH A 36 636 1178 HOH HOH . 
K 5 HOH A 37 637 1048 HOH HOH . 
K 5 HOH A 38 638 1109 HOH HOH . 
K 5 HOH A 39 639 1054 HOH HOH . 
K 5 HOH A 40 640 1083 HOH HOH . 
K 5 HOH A 41 641 1002 HOH HOH . 
K 5 HOH A 42 642 1120 HOH HOH . 
K 5 HOH A 43 643 1130 HOH HOH . 
K 5 HOH A 44 644 1159 HOH HOH . 
K 5 HOH A 45 645 1143 HOH HOH . 
K 5 HOH A 46 646 1009 HOH HOH . 
K 5 HOH A 47 647 1017 HOH HOH . 
K 5 HOH A 48 648 1057 HOH HOH . 
K 5 HOH A 49 649 1104 HOH HOH . 
K 5 HOH A 50 650 1061 HOH HOH . 
K 5 HOH A 51 651 1010 HOH HOH . 
K 5 HOH A 52 652 1056 HOH HOH . 
K 5 HOH A 53 653 1043 HOH HOH . 
K 5 HOH A 54 654 1058 HOH HOH . 
K 5 HOH A 55 655 1008 HOH HOH . 
K 5 HOH A 56 656 1016 HOH HOH . 
K 5 HOH A 57 657 1177 HOH HOH . 
K 5 HOH A 58 658 1040 HOH HOH . 
K 5 HOH A 59 659 1013 HOH HOH . 
K 5 HOH A 60 660 1072 HOH HOH . 
K 5 HOH A 61 661 1046 HOH HOH . 
K 5 HOH A 62 662 1042 HOH HOH . 
K 5 HOH A 63 663 1090 HOH HOH . 
K 5 HOH A 64 664 1050 HOH HOH . 
K 5 HOH A 65 665 1106 HOH HOH . 
K 5 HOH A 66 666 1024 HOH HOH . 
K 5 HOH A 67 667 1026 HOH HOH . 
K 5 HOH A 68 668 1127 HOH HOH . 
K 5 HOH A 69 669 1034 HOH HOH . 
K 5 HOH A 70 670 1098 HOH HOH . 
K 5 HOH A 71 671 1144 HOH HOH . 
K 5 HOH A 72 672 1021 HOH HOH . 
K 5 HOH A 73 673 1062 HOH HOH . 
K 5 HOH A 74 674 1029 HOH HOH . 
K 5 HOH A 75 675 1093 HOH HOH . 
K 5 HOH A 76 676 1020 HOH HOH . 
K 5 HOH A 77 677 1146 HOH HOH . 
K 5 HOH A 78 678 1171 HOH HOH . 
K 5 HOH A 79 679 1161 HOH HOH . 
K 5 HOH A 80 680 1035 HOH HOH . 
K 5 HOH A 81 681 1137 HOH HOH . 
K 5 HOH A 82 682 1138 HOH HOH . 
K 5 HOH A 83 683 1012 HOH HOH . 
K 5 HOH A 84 684 1075 HOH HOH . 
K 5 HOH A 85 685 1158 HOH HOH . 
K 5 HOH A 86 686 1164 HOH HOH . 
K 5 HOH A 87 687 1172 HOH HOH . 
K 5 HOH A 88 688 1175 HOH HOH . 
K 5 HOH A 89 689 1068 HOH HOH . 
K 5 HOH A 90 690 1004 HOH HOH . 
K 5 HOH A 91 691 1176 HOH HOH . 
K 5 HOH A 92 692 1102 HOH HOH . 
K 5 HOH A 93 693 1036 HOH HOH . 
K 5 HOH A 94 694 1174 HOH HOH . 
K 5 HOH A 95 695 1149 HOH HOH . 
K 5 HOH A 96 696 1094 HOH HOH . 
K 5 HOH A 97 697 1051 HOH HOH . 
K 5 HOH A 98 698 1074 HOH HOH . 
K 5 HOH A 99 699 1123 HOH HOH . 
K 5 HOH A 100 700 1103 HOH HOH . 
K 5 HOH A 101 701 1112 HOH HOH . 
K 5 HOH A 102 702 1039 HOH HOH . 
K 5 HOH A 103 703 1108 HOH HOH . 
K 5 HOH A 104 704 1087 HOH HOH . 
K 5 HOH A 105 705 1151 HOH HOH . 
K 5 HOH A 106 706 1027 HOH HOH . 
K 5 HOH A 107 707 1091 HOH HOH . 
K 5 HOH A 108 708 1117 HOH HOH . 
K 5 HOH A 109 709 1078 HOH HOH . 
K 5 HOH A 110 710 1155 HOH HOH . 
K 5 HOH A 111 711 1088 HOH HOH . 
K 5 HOH A 112 712 1047 HOH HOH . 
K 5 HOH A 113 713 1065 HOH HOH . 
K 5 HOH A 114 714 1148 HOH HOH . 
K 5 HOH A 115 715 1116 HOH HOH . 
K 5 HOH A 116 716 1152 HOH HOH . 
K 5 HOH A 117 717 1077 HOH HOH . 
K 5 HOH A 118 718 1115 HOH HOH . 
K 5 HOH A 119 719 1184 HOH HOH . 
K 5 HOH A 120 720 1105 HOH HOH . 
K 5 HOH A 121 721 1114 HOH HOH . 
K 5 HOH A 122 722 1049 HOH HOH . 
K 5 HOH A 123 723 1071 HOH HOH . 
K 5 HOH A 124 724 1189 HOH HOH . 
K 5 HOH A 125 725 1126 HOH HOH . 
K 5 HOH A 126 726 1001 HOH HOH . 
K 5 HOH A 127 727 1076 HOH HOH . 
K 5 HOH A 128 728 1194 HOH HOH . 
K 5 HOH A 129 729 1018 HOH HOH . 
K 5 HOH A 130 730 1122 HOH HOH . 
K 5 HOH A 131 731 1038 HOH HOH . 
K 5 HOH A 132 732 1066 HOH HOH . 
K 5 HOH A 133 733 1030 HOH HOH . 
K 5 HOH A 134 734 1110 HOH HOH . 
K 5 HOH A 135 735 1125 HOH HOH . 
K 5 HOH A 136 736 1011 HOH HOH . 
K 5 HOH A 137 737 1191 HOH HOH . 
K 5 HOH A 138 738 1107 HOH HOH . 
K 5 HOH A 139 739 1022 HOH HOH . 
K 5 HOH A 140 740 1032 HOH HOH . 
K 5 HOH A 141 741 1025 HOH HOH . 
K 5 HOH A 142 742 1095 HOH HOH . 
K 5 HOH A 143 743 1005 HOH HOH . 
K 5 HOH A 144 744 1192 HOH HOH . 
K 5 HOH A 145 745 1041 HOH HOH . 
K 5 HOH A 146 746 1086 HOH HOH . 
K 5 HOH A 147 747 1197 HOH HOH . 
K 5 HOH A 148 748 1092 HOH HOH . 
K 5 HOH A 149 749 1187 HOH HOH . 
K 5 HOH A 150 750 1085 HOH HOH . 
K 5 HOH A 151 751 1156 HOH HOH . 
K 5 HOH A 152 752 1082 HOH HOH . 
K 5 HOH A 153 753 1169 HOH HOH . 
K 5 HOH A 154 754 1037 HOH HOH . 
K 5 HOH A 155 755 1150 HOH HOH . 
K 5 HOH A 156 756 1045 HOH HOH . 
K 5 HOH A 157 757 1157 HOH HOH . 
K 5 HOH A 158 758 1096 HOH HOH . 
K 5 HOH A 159 759 1067 HOH HOH . 
K 5 HOH A 160 760 1142 HOH HOH . 
K 5 HOH A 161 761 1196 HOH HOH . 
K 5 HOH A 162 762 1180 HOH HOH . 
K 5 HOH A 163 763 1170 HOH HOH . 
K 5 HOH A 164 764 1023 HOH HOH . 
K 5 HOH A 165 765 1154 HOH HOH . 
K 5 HOH A 166 766 1198 HOH HOH . 
K 5 HOH A 167 767 1118 HOH HOH . 
K 5 HOH A 168 768 1081 HOH HOH . 
K 5 HOH A 169 769 1060 HOH HOH . 
K 5 HOH A 170 770 1133 HOH HOH . 
K 5 HOH A 171 771 1166 HOH HOH . 
K 5 HOH A 172 772 1141 HOH HOH . 
K 5 HOH A 173 773 1153 HOH HOH . 
K 5 HOH A 174 774 1163 HOH HOH . 
K 5 HOH A 175 775 1099 HOH HOH . 
K 5 HOH A 176 776 1173 HOH HOH . 
K 5 HOH A 177 777 1136 HOH HOH . 
K 5 HOH A 178 778 1119 HOH HOH . 
K 5 HOH A 179 779 1147 HOH HOH . 
K 5 HOH A 180 780 1185 HOH HOH . 
K 5 HOH A 181 781 1165 HOH HOH . 
K 5 HOH A 182 782 1113 HOH HOH . 
K 5 HOH A 183 783 1188 HOH HOH . 
K 5 HOH A 184 784 1168 HOH HOH . 
K 5 HOH A 185 785 1167 HOH HOH . 
K 5 HOH A 186 786 1179 HOH HOH . 
K 5 HOH A 187 787 1183 HOH HOH . 
K 5 HOH A 188 788 1193 HOH HOH . 
K 5 HOH A 189 789 1199 HOH HOH . 
K 5 HOH A 190 790 1084 HOH HOH . 
K 5 HOH A 191 791 1139 HOH HOH . 
K 5 HOH A 192 792 1190 HOH HOH . 
K 5 HOH A 193 793 1181 HOH HOH . 
K 5 HOH A 194 794 1124 HOH HOH . 
K 5 HOH A 195 795 1195 HOH HOH . 
K 5 HOH A 196 796 1162 HOH HOH . 
K 5 HOH A 197 797 1186 HOH HOH . 
K 5 HOH A 198 798 1059 HOH HOH . 
K 5 HOH A 199 799 1132 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 . . . G 3 -34.408 -23.024 -7.051 1 40.83 ? C1 GOL 506 A 1 
HETATM 2 O O1 GOL . . . G 3 -33.775 -23.907 -6.13 1 34.46 ? O1 GOL 506 A 1 
HETATM 3 C C2 GOL . . . G 3 -35.902 -22.886 -6.766 1 43.35 ? C2 GOL 506 A 1 
HETATM 4 O O2 GOL . . . G 3 -36.518 -24.175 -6.802 1 46.09 ? O2 GOL 506 A 1 
HETATM 5 C C3 GOL . . . G 3 -36.51 -22.027 -7.876 1 44.97 ? C3 GOL 506 A 1 
HETATM 6 O O3 GOL . . . G 3 -37.913 -21.864 -7.643 1 47.23 ? O3 GOL 506 A 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           26 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           6 
#