data_7YB8 # _model_server_result.job_id CdLPcA3J72lLbKMPSBpUVQ _model_server_result.datetime_utc '2024-10-20 01:26:01' _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 7yb8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1001}' # _entry.id 7YB8 # _exptl.entry_id 7YB8 _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 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 90 _cell.entry_id 7YB8 _cell.length_a 49.879 _cell.length_b 91.063 _cell.length_c 122.351 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7YB8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _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 # _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 # 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 312 A CYS 641 1_555 A SG CYS 319 A CYS 648 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 B SG CYS 16 B CYS 101 1_555 B SG CYS 25 B CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc1 A NE2 HIS 350 A HIS 679 1_555 E MN MN . A MN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc2 A NE2 HIS 396 A HIS 725 1_555 E MN MN . A MN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc3 E MN MN . A MN 1003 1_555 F O3 2HG . A 2HG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc4 E MN MN . A MN 1003 1_555 F O2 2HG . A 2HG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? # _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 146 n n C1 C2 GOL sing 147 n n C1 H11 GOL sing 148 n n C1 H12 GOL sing 149 n n O1 HO1 GOL sing 150 n n C2 O2 GOL sing 151 n n C2 C3 GOL sing 152 n n C2 H2 GOL sing 153 n n O2 HO2 GOL sing 154 n n C3 O3 GOL sing 155 n n C3 H31 GOL sing 156 n n C3 H32 GOL sing 157 n n O3 HO3 GOL sing 158 n n # _atom_sites.entry_id 7YB8 _atom_sites.fract_transf_matrix[1][1] 0.020049 _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] 0.010981 _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] 0.008173 _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 C 3 GOL A 1 1001 1001 GOL GOL . D 3 GOL A 1 1002 1101 GOL GOL . E 4 MN A 1 1003 801 MN MN . F 5 2HG A 1 1004 901 2HG LIG . G 6 HOH A 1 1101 63 HOH HOH . G 6 HOH A 2 1102 106 HOH HOH . G 6 HOH A 3 1103 58 HOH HOH . G 6 HOH A 4 1104 5 HOH HOH . G 6 HOH A 5 1105 114 HOH HOH . G 6 HOH A 6 1106 60 HOH HOH . G 6 HOH A 7 1107 67 HOH HOH . G 6 HOH A 8 1108 54 HOH HOH . G 6 HOH A 9 1109 53 HOH HOH . G 6 HOH A 10 1110 62 HOH HOH . G 6 HOH A 11 1111 3 HOH HOH . G 6 HOH A 12 1112 20 HOH HOH . G 6 HOH A 13 1113 10 HOH HOH . G 6 HOH A 14 1114 8 HOH HOH . G 6 HOH A 15 1115 80 HOH HOH . G 6 HOH A 16 1116 32 HOH HOH . G 6 HOH A 17 1117 26 HOH HOH . G 6 HOH A 18 1118 45 HOH HOH . G 6 HOH A 19 1119 31 HOH HOH . G 6 HOH A 20 1120 69 HOH HOH . G 6 HOH A 21 1121 4 HOH HOH . G 6 HOH A 22 1122 14 HOH HOH . G 6 HOH A 23 1123 74 HOH HOH . G 6 HOH A 24 1124 48 HOH HOH . G 6 HOH A 25 1125 40 HOH HOH . G 6 HOH A 26 1126 124 HOH HOH . G 6 HOH A 27 1127 13 HOH HOH . G 6 HOH A 28 1128 77 HOH HOH . G 6 HOH A 29 1129 111 HOH HOH . G 6 HOH A 30 1130 17 HOH HOH . G 6 HOH A 31 1131 34 HOH HOH . G 6 HOH A 32 1132 47 HOH HOH . G 6 HOH A 33 1133 2 HOH HOH . G 6 HOH A 34 1134 28 HOH HOH . G 6 HOH A 35 1135 57 HOH HOH . G 6 HOH A 36 1136 36 HOH HOH . G 6 HOH A 37 1137 113 HOH HOH . G 6 HOH A 38 1138 30 HOH HOH . G 6 HOH A 39 1139 16 HOH HOH . G 6 HOH A 40 1140 24 HOH HOH . G 6 HOH A 41 1141 65 HOH HOH . G 6 HOH A 42 1142 103 HOH HOH . G 6 HOH A 43 1143 18 HOH HOH . G 6 HOH A 44 1144 46 HOH HOH . G 6 HOH A 45 1145 52 HOH HOH . G 6 HOH A 46 1146 23 HOH HOH . G 6 HOH A 47 1147 64 HOH HOH . G 6 HOH A 48 1148 81 HOH HOH . G 6 HOH A 49 1149 29 HOH HOH . G 6 HOH A 50 1150 86 HOH HOH . G 6 HOH A 51 1151 42 HOH HOH . G 6 HOH A 52 1152 12 HOH HOH . G 6 HOH A 53 1153 120 HOH HOH . G 6 HOH A 54 1154 72 HOH HOH . G 6 HOH A 55 1155 79 HOH HOH . G 6 HOH A 56 1156 39 HOH HOH . G 6 HOH A 57 1157 105 HOH HOH . G 6 HOH A 58 1158 56 HOH HOH . G 6 HOH A 59 1159 6 HOH HOH . G 6 HOH A 60 1160 123 HOH HOH . G 6 HOH A 61 1161 71 HOH HOH . G 6 HOH A 62 1162 130 HOH HOH . G 6 HOH A 63 1163 41 HOH HOH . G 6 HOH A 64 1164 55 HOH HOH . G 6 HOH A 65 1165 75 HOH HOH . G 6 HOH A 66 1166 25 HOH HOH . G 6 HOH A 67 1167 99 HOH HOH . G 6 HOH A 68 1168 89 HOH HOH . G 6 HOH A 69 1169 118 HOH HOH . G 6 HOH A 70 1170 110 HOH HOH . G 6 HOH A 71 1171 19 HOH HOH . G 6 HOH A 72 1172 121 HOH HOH . G 6 HOH A 73 1173 15 HOH HOH . G 6 HOH A 74 1174 43 HOH HOH . G 6 HOH A 75 1175 78 HOH HOH . G 6 HOH A 76 1176 122 HOH HOH . G 6 HOH A 77 1177 90 HOH HOH . G 6 HOH A 78 1178 49 HOH HOH . G 6 HOH A 79 1179 68 HOH HOH . G 6 HOH A 80 1180 104 HOH HOH . G 6 HOH A 81 1181 107 HOH HOH . G 6 HOH A 82 1182 131 HOH HOH . G 6 HOH A 83 1183 11 HOH HOH . G 6 HOH A 84 1184 109 HOH HOH . G 6 HOH A 85 1185 92 HOH HOH . G 6 HOH A 86 1186 116 HOH HOH . G 6 HOH A 87 1187 91 HOH HOH . G 6 HOH A 88 1188 112 HOH HOH . G 6 HOH A 89 1189 93 HOH HOH . G 6 HOH A 90 1190 132 HOH HOH . G 6 HOH A 91 1191 87 HOH HOH . G 6 HOH A 92 1192 83 HOH HOH . G 6 HOH A 93 1193 134 HOH HOH . G 6 HOH A 94 1194 127 HOH HOH . G 6 HOH A 95 1195 128 HOH HOH . G 6 HOH A 96 1196 94 HOH HOH . G 6 HOH A 97 1197 33 HOH HOH . G 6 HOH A 98 1198 129 HOH HOH . G 6 HOH A 99 1199 82 HOH HOH . G 6 HOH A 100 1200 133 HOH HOH . G 6 HOH A 101 1201 98 HOH HOH . G 6 HOH A 102 1202 85 HOH HOH . G 6 HOH A 103 1203 44 HOH HOH . G 6 HOH A 104 1204 102 HOH HOH . G 6 HOH A 105 1205 76 HOH HOH . G 6 HOH A 106 1206 115 HOH HOH . G 6 HOH A 107 1207 108 HOH HOH . G 6 HOH A 108 1208 50 HOH HOH . G 6 HOH A 109 1209 66 HOH HOH . H 6 HOH B 1 201 96 HOH HOH . H 6 HOH B 2 202 1 HOH HOH . H 6 HOH B 3 203 61 HOH HOH . H 6 HOH B 4 204 38 HOH HOH . H 6 HOH B 5 205 100 HOH HOH . H 6 HOH B 6 206 27 HOH HOH . H 6 HOH B 7 207 119 HOH HOH . H 6 HOH B 8 208 125 HOH HOH . H 6 HOH B 9 209 101 HOH HOH . H 6 HOH B 10 210 126 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 . . . C 3 70.097 22.808 49.399 1 57.74 ? C1 GOL 1001 A 1 HETATM 2 O O1 GOL . . . C 3 71.388 23.121 48.944 1 56.86 ? O1 GOL 1001 A 1 HETATM 3 C C2 GOL . . . C 3 69.115 23.705 48.611 1 57.35 ? C2 GOL 1001 A 1 HETATM 4 O O2 GOL . . . C 3 68.931 24.918 49.215 1 59.62 ? O2 GOL 1001 A 1 HETATM 5 C C3 GOL . . . C 3 67.817 22.874 48.517 1 56.69 ? C3 GOL 1001 A 1 HETATM 6 O O3 GOL . . . C 3 66.753 23.767 48.665 1 58.27 ? O3 GOL 1001 A 1 HETATM 7 H H11 GOL . . . C 3 69.986 22.968 50.349 1 69.91 ? H11 GOL 1001 A 1 HETATM 8 H H12 GOL . . . C 3 69.866 21.877 49.257 1 69.91 ? H12 GOL 1001 A 1 HETATM 9 H HO1 GOL . . . C 3 71.91 22.951 49.587 1 68.86 ? HO1 GOL 1001 A 1 HETATM 10 H H2 GOL . . . C 3 69.459 23.907 47.727 1 69.44 ? H2 GOL 1001 A 1 HETATM 11 H HO2 GOL . . . C 3 68.826 25.5 48.582 1 72.17 ? HO2 GOL 1001 A 1 HETATM 12 H HO3 GOL . . . C 3 66.027 23.326 48.633 1 70.55 ? HO3 GOL 1001 A 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 12 #