data_3VV6
#
_model_server_result.job_id            rC6t4wg7_YRHRAVd76xgXA 
_model_server_result.datetime_utc      '2024-11-24 12:35:25' 
_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          3vv6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":508}' 
#
_entry.id    3VV6 
#
_exptl.entry_id    3VV6 
_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    4 
_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            3VV6 
_cell.length_a            102.491 
_cell.length_b            102.491 
_cell.length_c            170.156 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VV6 
_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,L 
_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 
? 3 J 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? 
disulf ? disulf2 A SG CYS 240 A CYS 217 1_555 A SG CYS 405 A CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf3 A SG CYS 292 A CYS 269 1_555 A SG CYS 342 A CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
#
_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 164 n n 
C1 C2 GOL sing 165 n n 
C1 H11 GOL sing 166 n n 
C1 H12 GOL sing 167 n n 
O1 HO1 GOL sing 168 n n 
C2 O2 GOL sing 169 n n 
C2 C3 GOL sing 170 n n 
C2 H2 GOL sing 171 n n 
O2 HO2 GOL sing 172 n n 
C3 O3 GOL sing 173 n n 
C3 H31 GOL sing 174 n n 
C3 H32 GOL sing 175 n n 
O3 HO3 GOL sing 176 n n 
#
_atom_sites.entry_id                     3VV6 
_atom_sites.fract_transf_matrix[1][1]    0.009757 
_atom_sites.fract_transf_matrix[1][2]    0.005633 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011266 
_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]    0.005877 
_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 1 506 601 GOL GOL . 
H 3 GOL A 1 507 602 GOL GOL . 
I 3 GOL A 1 508 603 GOL GOL . 
J 3 GOL A 1 509 604 GOL GOL . 
K 4 B00 A 1 510 701 B00 B00 . 
L 5 HOH A 1 1001 1001 HOH HOH . 
L 5 HOH A 2 1002 1002 HOH HOH . 
L 5 HOH A 3 1003 1003 HOH HOH . 
L 5 HOH A 4 1004 1004 HOH HOH . 
L 5 HOH A 5 1005 1005 HOH HOH . 
L 5 HOH A 6 1006 1006 HOH HOH . 
L 5 HOH A 7 1007 1007 HOH HOH . 
L 5 HOH A 8 1008 1008 HOH HOH . 
L 5 HOH A 9 1009 1009 HOH HOH . 
L 5 HOH A 10 1010 1010 HOH HOH . 
L 5 HOH A 11 1011 1011 HOH HOH . 
L 5 HOH A 12 1012 1012 HOH HOH . 
L 5 HOH A 13 1013 1013 HOH HOH . 
L 5 HOH A 14 1014 1014 HOH HOH . 
L 5 HOH A 15 1015 1015 HOH HOH . 
L 5 HOH A 16 1016 1016 HOH HOH . 
L 5 HOH A 17 1017 1017 HOH HOH . 
L 5 HOH A 18 1018 1018 HOH HOH . 
L 5 HOH A 19 1019 1019 HOH HOH . 
L 5 HOH A 20 1020 1020 HOH HOH . 
L 5 HOH A 21 1021 1021 HOH HOH . 
L 5 HOH A 22 1022 1022 HOH HOH . 
L 5 HOH A 23 1023 1023 HOH HOH . 
L 5 HOH A 24 1024 1025 HOH HOH . 
L 5 HOH A 25 1025 1026 HOH HOH . 
L 5 HOH A 26 1026 1027 HOH HOH . 
L 5 HOH A 27 1027 1028 HOH HOH . 
L 5 HOH A 28 1028 1029 HOH HOH . 
L 5 HOH A 29 1029 1030 HOH HOH . 
L 5 HOH A 30 1030 1032 HOH HOH . 
L 5 HOH A 31 1031 1034 HOH HOH . 
L 5 HOH A 32 1032 1035 HOH HOH . 
L 5 HOH A 33 1033 1036 HOH HOH . 
L 5 HOH A 34 1034 1037 HOH HOH . 
L 5 HOH A 35 1035 1038 HOH HOH . 
L 5 HOH A 36 1036 1039 HOH HOH . 
L 5 HOH A 37 1037 1040 HOH HOH . 
L 5 HOH A 38 1038 1041 HOH HOH . 
L 5 HOH A 39 1039 1042 HOH HOH . 
L 5 HOH A 40 1040 1043 HOH HOH . 
L 5 HOH A 41 1041 1044 HOH HOH . 
L 5 HOH A 42 1042 1045 HOH HOH . 
L 5 HOH A 43 1043 1046 HOH HOH . 
L 5 HOH A 44 1044 1047 HOH HOH . 
L 5 HOH A 45 1045 1048 HOH HOH . 
L 5 HOH A 46 1046 1049 HOH HOH . 
L 5 HOH A 47 1047 1050 HOH HOH . 
L 5 HOH A 48 1048 1051 HOH HOH . 
L 5 HOH A 49 1049 1052 HOH HOH . 
L 5 HOH A 50 1050 1053 HOH HOH . 
L 5 HOH A 51 1051 1054 HOH HOH . 
L 5 HOH A 52 1052 1055 HOH HOH . 
L 5 HOH A 53 1053 1056 HOH HOH . 
L 5 HOH A 54 1054 1057 HOH HOH . 
L 5 HOH A 55 1055 1058 HOH HOH . 
L 5 HOH A 56 1056 1059 HOH HOH . 
L 5 HOH A 57 1057 1060 HOH HOH . 
L 5 HOH A 58 1058 1061 HOH HOH . 
L 5 HOH A 59 1059 1062 HOH HOH . 
L 5 HOH A 60 1060 1063 HOH HOH . 
L 5 HOH A 61 1061 1064 HOH HOH . 
L 5 HOH A 62 1062 1066 HOH HOH . 
L 5 HOH A 63 1063 1067 HOH HOH . 
L 5 HOH A 64 1064 1068 HOH HOH . 
L 5 HOH A 65 1065 1069 HOH HOH . 
L 5 HOH A 66 1066 1070 HOH HOH . 
L 5 HOH A 67 1067 1072 HOH HOH . 
L 5 HOH A 68 1068 1073 HOH HOH . 
L 5 HOH A 69 1069 1074 HOH HOH . 
L 5 HOH A 70 1070 1075 HOH HOH . 
L 5 HOH A 71 1071 1076 HOH HOH . 
L 5 HOH A 72 1072 1078 HOH HOH . 
L 5 HOH A 73 1073 1079 HOH HOH . 
L 5 HOH A 74 1074 1080 HOH HOH . 
L 5 HOH A 75 1075 1081 HOH HOH . 
L 5 HOH A 76 1076 1082 HOH HOH . 
L 5 HOH A 77 1077 1083 HOH HOH . 
L 5 HOH A 78 1078 1084 HOH HOH . 
L 5 HOH A 79 1079 1085 HOH HOH . 
L 5 HOH A 80 1080 1086 HOH HOH . 
L 5 HOH A 81 1081 1087 HOH HOH . 
L 5 HOH A 82 1082 1088 HOH HOH . 
L 5 HOH A 83 1083 1091 HOH HOH . 
L 5 HOH A 84 1084 1092 HOH HOH . 
L 5 HOH A 85 1085 1093 HOH HOH . 
L 5 HOH A 86 1086 1094 HOH HOH . 
L 5 HOH A 87 1087 1095 HOH HOH . 
L 5 HOH A 88 1088 1096 HOH HOH . 
L 5 HOH A 89 1089 1097 HOH HOH . 
L 5 HOH A 90 1090 1098 HOH HOH . 
L 5 HOH A 91 1091 1099 HOH HOH . 
L 5 HOH A 92 1092 1100 HOH HOH . 
L 5 HOH A 93 1093 1101 HOH HOH . 
L 5 HOH A 94 1094 1102 HOH HOH . 
L 5 HOH A 95 1095 1103 HOH HOH . 
L 5 HOH A 96 1096 1104 HOH HOH . 
L 5 HOH A 97 1097 1105 HOH HOH . 
L 5 HOH A 98 1098 1106 HOH HOH . 
L 5 HOH A 99 1099 1107 HOH HOH . 
L 5 HOH A 100 1100 1108 HOH HOH . 
L 5 HOH A 101 1101 1110 HOH HOH . 
L 5 HOH A 102 1102 1111 HOH HOH . 
L 5 HOH A 103 1103 1112 HOH HOH . 
L 5 HOH A 104 1104 1113 HOH HOH . 
L 5 HOH A 105 1105 1115 HOH HOH . 
L 5 HOH A 106 1106 1118 HOH HOH . 
L 5 HOH A 107 1107 1120 HOH HOH . 
L 5 HOH A 108 1108 1121 HOH HOH . 
L 5 HOH A 109 1109 1122 HOH HOH . 
L 5 HOH A 110 1110 1124 HOH HOH . 
L 5 HOH A 111 1111 1126 HOH HOH . 
L 5 HOH A 112 1112 1127 HOH HOH . 
L 5 HOH A 113 1113 1128 HOH HOH . 
L 5 HOH A 114 1114 1129 HOH HOH . 
L 5 HOH A 115 1115 1132 HOH HOH . 
L 5 HOH A 116 1116 1133 HOH HOH . 
L 5 HOH A 117 1117 1135 HOH HOH . 
L 5 HOH A 118 1118 1136 HOH HOH . 
L 5 HOH A 119 1119 1138 HOH HOH . 
L 5 HOH A 120 1120 1140 HOH HOH . 
L 5 HOH A 121 1121 1141 HOH HOH . 
L 5 HOH A 122 1122 1142 HOH HOH . 
L 5 HOH A 123 1123 1144 HOH HOH . 
L 5 HOH A 124 1124 1146 HOH HOH . 
L 5 HOH A 125 1125 1148 HOH HOH . 
L 5 HOH A 126 1126 1149 HOH HOH . 
L 5 HOH A 127 1127 1150 HOH HOH . 
L 5 HOH A 128 1128 1151 HOH HOH . 
L 5 HOH A 129 1129 1152 HOH HOH . 
L 5 HOH A 130 1130 1153 HOH HOH . 
L 5 HOH A 131 1131 1154 HOH HOH . 
L 5 HOH A 132 1132 1155 HOH HOH . 
L 5 HOH A 133 1133 1156 HOH HOH . 
L 5 HOH A 134 1134 1157 HOH HOH . 
L 5 HOH A 135 1135 1158 HOH HOH . 
L 5 HOH A 136 1136 1159 HOH HOH . 
L 5 HOH A 137 1137 1160 HOH HOH . 
L 5 HOH A 138 1138 1161 HOH HOH . 
L 5 HOH A 139 1139 1162 HOH HOH . 
L 5 HOH A 140 1140 1163 HOH HOH . 
L 5 HOH A 141 1141 1166 HOH HOH . 
L 5 HOH A 142 1142 1168 HOH HOH . 
L 5 HOH A 143 1143 1169 HOH HOH . 
L 5 HOH A 144 1144 1170 HOH HOH . 
L 5 HOH A 145 1145 1171 HOH HOH . 
L 5 HOH A 146 1146 1172 HOH HOH . 
L 5 HOH A 147 1147 1173 HOH HOH . 
L 5 HOH A 148 1148 1175 HOH HOH . 
L 5 HOH A 149 1149 1177 HOH HOH . 
L 5 HOH A 150 1150 1178 HOH HOH . 
L 5 HOH A 151 1151 1179 HOH HOH . 
L 5 HOH A 152 1152 1180 HOH HOH . 
L 5 HOH A 153 1153 1181 HOH HOH . 
L 5 HOH A 154 1154 1182 HOH HOH . 
L 5 HOH A 155 1155 1184 HOH HOH . 
L 5 HOH A 156 1156 1185 HOH HOH . 
L 5 HOH A 157 1157 1186 HOH HOH . 
L 5 HOH A 158 1158 1188 HOH HOH . 
L 5 HOH A 159 1159 1190 HOH HOH . 
L 5 HOH A 160 1160 1192 HOH HOH . 
L 5 HOH A 161 1161 1193 HOH HOH . 
L 5 HOH A 162 1162 1194 HOH HOH . 
L 5 HOH A 163 1163 1195 HOH HOH . 
L 5 HOH A 164 1164 1197 HOH HOH . 
L 5 HOH A 165 1165 1198 HOH HOH . 
L 5 HOH A 166 1166 1199 HOH HOH . 
L 5 HOH A 167 1167 1201 HOH HOH . 
L 5 HOH A 168 1168 1203 HOH HOH . 
L 5 HOH A 169 1169 1204 HOH HOH . 
L 5 HOH A 170 1170 1205 HOH HOH . 
L 5 HOH A 171 1171 1206 HOH HOH . 
L 5 HOH A 172 1172 1208 HOH HOH . 
L 5 HOH A 173 1173 1209 HOH HOH . 
L 5 HOH A 174 1174 1211 HOH HOH . 
L 5 HOH A 175 1175 1212 HOH HOH . 
L 5 HOH A 176 1176 1215 HOH HOH . 
L 5 HOH A 177 1177 1216 HOH HOH . 
L 5 HOH A 178 1178 1217 HOH HOH . 
L 5 HOH A 179 1179 1218 HOH HOH . 
L 5 HOH A 180 1180 1219 HOH HOH . 
L 5 HOH A 181 1181 1220 HOH HOH . 
L 5 HOH A 182 1182 1221 HOH HOH . 
L 5 HOH A 183 1183 1222 HOH HOH . 
L 5 HOH A 184 1184 1224 HOH HOH . 
L 5 HOH A 185 1185 1225 HOH HOH . 
L 5 HOH A 186 1186 1226 HOH HOH . 
L 5 HOH A 187 1187 1227 HOH HOH . 
L 5 HOH A 188 1188 1229 HOH HOH . 
L 5 HOH A 189 1189 1230 HOH HOH . 
L 5 HOH A 190 1190 1232 HOH HOH . 
L 5 HOH A 191 1191 1233 HOH HOH . 
L 5 HOH A 192 1192 1234 HOH HOH . 
L 5 HOH A 193 1193 1235 HOH HOH . 
L 5 HOH A 194 1194 1237 HOH HOH . 
L 5 HOH A 195 1195 1238 HOH HOH . 
L 5 HOH A 196 1196 1239 HOH HOH . 
L 5 HOH A 197 1197 1241 HOH HOH . 
L 5 HOH A 198 1198 1243 HOH HOH . 
L 5 HOH A 199 1199 1244 HOH HOH . 
L 5 HOH A 200 1200 1245 HOH HOH . 
L 5 HOH A 201 1201 1246 HOH HOH . 
L 5 HOH A 202 1202 1247 HOH HOH . 
L 5 HOH A 203 1203 1248 HOH HOH . 
L 5 HOH A 204 1204 1249 HOH HOH . 
L 5 HOH A 205 1205 1250 HOH HOH . 
L 5 HOH A 206 1206 1251 HOH HOH . 
L 5 HOH A 207 1207 1252 HOH HOH . 
L 5 HOH A 208 1208 1253 HOH HOH . 
L 5 HOH A 209 1209 1254 HOH HOH . 
L 5 HOH A 210 1210 1255 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 . . . I 3 7.342 37.802 21.394 1 49.6 ? C1 GOL 508 A 1 
HETATM 2 O O1 GOL . . . I 3 6.014 37.913 21.853 1 51.71 ? O1 GOL 508 A 1 
HETATM 3 C C2 GOL . . . I 3 8.122 39.051 21.789 1 49.69 ? C2 GOL 508 A 1 
HETATM 4 O O2 GOL . . . I 3 9.416 38.992 21.233 1 48.28 ? O2 GOL 508 A 1 
HETATM 5 C C3 GOL . . . I 3 7.4 40.287 21.268 1 48.12 ? C3 GOL 508 A 1 
HETATM 6 O O3 GOL . . . I 3 7.674 41.383 22.112 1 49.58 ? O3 GOL 508 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           6 
#