data_5J1N
#
_model_server_result.job_id            ZuXP19nHCdeCYYw1aw3YCg 
_model_server_result.datetime_utc      '2024-11-09 02:48:45' 
_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          5j1n 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1002}' 
#
_entry.id    5J1N 
#
_exptl.entry_id    5J1N 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.174 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4S)-2-METHYL-2,4-PENTANEDIOL 
_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            5J1N 
_cell.length_a            51.5 
_cell.length_b            51.5 
_cell.length_c            143 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5J1N 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_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
metalc ? metalc1 A OD2 ASP 90 A ASP 89 1_555 B MN MN3 . A MN3 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc2 A OE1 GLU 103 A GLU 102 1_555 B MN MN3 . A MN3 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? 
metalc ? metalc3 B MN MN3 . A MN3 1001 1_555 E O HOH . A HOH 1119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? 
metalc ? metalc4 B MN MN3 . A MN3 1001 1_555 E O HOH . A HOH 1178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? 
metalc ? metalc5 B MN MN3 . A MN3 1001 1_555 E O HOH . A HOH 1255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? 
metalc ? metalc6 B MN MN3 . A MN3 1001 1_555 E O HOH . A HOH 1293 6_454 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? 
#
_chem_comp.formula           'C6 H14 O2' 
_chem_comp.formula_weight    118.174 
_chem_comp.id                MPD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (4S)-2-METHYL-2,4-PENTANEDIOL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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 C2 MPD sing 237 n n 
C1 H11 MPD sing 238 n n 
C1 H12 MPD sing 239 n n 
C1 H13 MPD sing 240 n n 
C2 O2 MPD sing 241 n n 
C2 CM MPD sing 242 n n 
C2 C3 MPD sing 243 n n 
O2 HO2 MPD sing 244 n n 
CM HM1 MPD sing 245 n n 
CM HM2 MPD sing 246 n n 
CM HM3 MPD sing 247 n n 
C3 C4 MPD sing 248 n n 
C3 H31 MPD sing 249 n n 
C3 H32 MPD sing 250 n n 
C4 O4 MPD sing 251 n n 
C4 C5 MPD sing 252 n n 
C4 H4 MPD sing 253 n n 
O4 HO4 MPD sing 254 n n 
C5 H51 MPD sing 255 n n 
C5 H52 MPD sing 256 n n 
C5 H53 MPD sing 257 n n 
#
_atom_sites.entry_id                     5J1N 
_atom_sites.fract_transf_matrix[1][1]    0.019417 
_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]    0.019417 
_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]    0.006993 
_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 MN3 A 1 1001 1001 MN3 MN3 . 
C 3 MPD A 1 1002 1 MPD MPD . 
D 3 MPD A 1 1003 2 MPD MPD . 
E 4 HOH A 1 1101 100 HOH HOH . 
E 4 HOH A 2 1102 186 HOH HOH . 
E 4 HOH A 3 1103 162 HOH HOH . 
E 4 HOH A 4 1104 183 HOH HOH . 
E 4 HOH A 5 1105 143 HOH HOH . 
E 4 HOH A 6 1106 49 HOH HOH . 
E 4 HOH A 7 1107 76 HOH HOH . 
E 4 HOH A 8 1108 36 HOH HOH . 
E 4 HOH A 9 1109 19 HOH HOH . 
E 4 HOH A 10 1110 149 HOH HOH . 
E 4 HOH A 11 1111 84 HOH HOH . 
E 4 HOH A 12 1112 163 HOH HOH . 
E 4 HOH A 13 1113 154 HOH HOH . 
E 4 HOH A 14 1114 95 HOH HOH . 
E 4 HOH A 15 1115 204 HOH HOH . 
E 4 HOH A 16 1116 124 HOH HOH . 
E 4 HOH A 17 1117 73 HOH HOH . 
E 4 HOH A 18 1118 129 HOH HOH . 
E 4 HOH A 19 1119 21 HOH HOH . 
E 4 HOH A 20 1120 115 HOH HOH . 
E 4 HOH A 21 1121 97 HOH HOH . 
E 4 HOH A 22 1122 109 HOH HOH . 
E 4 HOH A 23 1123 14 HOH HOH . 
E 4 HOH A 24 1124 87 HOH HOH . 
E 4 HOH A 25 1125 116 HOH HOH . 
E 4 HOH A 26 1126 80 HOH HOH . 
E 4 HOH A 27 1127 12 HOH HOH . 
E 4 HOH A 28 1128 98 HOH HOH . 
E 4 HOH A 29 1129 172 HOH HOH . 
E 4 HOH A 30 1130 132 HOH HOH . 
E 4 HOH A 31 1131 126 HOH HOH . 
E 4 HOH A 32 1132 184 HOH HOH . 
E 4 HOH A 33 1133 54 HOH HOH . 
E 4 HOH A 34 1134 63 HOH HOH . 
E 4 HOH A 35 1135 160 HOH HOH . 
E 4 HOH A 36 1136 168 HOH HOH . 
E 4 HOH A 37 1137 64 HOH HOH . 
E 4 HOH A 38 1138 77 HOH HOH . 
E 4 HOH A 39 1139 161 HOH HOH . 
E 4 HOH A 40 1140 20 HOH HOH . 
E 4 HOH A 41 1141 48 HOH HOH . 
E 4 HOH A 42 1142 23 HOH HOH . 
E 4 HOH A 43 1143 101 HOH HOH . 
E 4 HOH A 44 1144 8 HOH HOH . 
E 4 HOH A 45 1145 57 HOH HOH . 
E 4 HOH A 46 1146 60 HOH HOH . 
E 4 HOH A 47 1147 3 HOH HOH . 
E 4 HOH A 48 1148 6 HOH HOH . 
E 4 HOH A 49 1149 102 HOH HOH . 
E 4 HOH A 50 1150 94 HOH HOH . 
E 4 HOH A 51 1151 55 HOH HOH . 
E 4 HOH A 52 1152 40 HOH HOH . 
E 4 HOH A 53 1153 190 HOH HOH . 
E 4 HOH A 54 1154 7 HOH HOH . 
E 4 HOH A 55 1155 45 HOH HOH . 
E 4 HOH A 56 1156 121 HOH HOH . 
E 4 HOH A 57 1157 182 HOH HOH . 
E 4 HOH A 58 1158 192 HOH HOH . 
E 4 HOH A 59 1159 114 HOH HOH . 
E 4 HOH A 60 1160 188 HOH HOH . 
E 4 HOH A 61 1161 41 HOH HOH . 
E 4 HOH A 62 1162 15 HOH HOH . 
E 4 HOH A 63 1163 166 HOH HOH . 
E 4 HOH A 64 1164 71 HOH HOH . 
E 4 HOH A 65 1165 86 HOH HOH . 
E 4 HOH A 66 1166 105 HOH HOH . 
E 4 HOH A 67 1167 61 HOH HOH . 
E 4 HOH A 68 1168 44 HOH HOH . 
E 4 HOH A 69 1169 176 HOH HOH . 
E 4 HOH A 70 1170 11 HOH HOH . 
E 4 HOH A 71 1171 93 HOH HOH . 
E 4 HOH A 72 1172 70 HOH HOH . 
E 4 HOH A 73 1173 37 HOH HOH . 
E 4 HOH A 74 1174 108 HOH HOH . 
E 4 HOH A 75 1175 194 HOH HOH . 
E 4 HOH A 76 1176 27 HOH HOH . 
E 4 HOH A 77 1177 34 HOH HOH . 
E 4 HOH A 78 1178 16 HOH HOH . 
E 4 HOH A 79 1179 79 HOH HOH . 
E 4 HOH A 80 1180 140 HOH HOH . 
E 4 HOH A 81 1181 137 HOH HOH . 
E 4 HOH A 82 1182 158 HOH HOH . 
E 4 HOH A 83 1183 155 HOH HOH . 
E 4 HOH A 84 1184 144 HOH HOH . 
E 4 HOH A 85 1185 81 HOH HOH . 
E 4 HOH A 86 1186 2 HOH HOH . 
E 4 HOH A 87 1187 38 HOH HOH . 
E 4 HOH A 88 1188 173 HOH HOH . 
E 4 HOH A 89 1189 17 HOH HOH . 
E 4 HOH A 90 1190 133 HOH HOH . 
E 4 HOH A 91 1191 159 HOH HOH . 
E 4 HOH A 92 1192 189 HOH HOH . 
E 4 HOH A 93 1193 68 HOH HOH . 
E 4 HOH A 94 1194 62 HOH HOH . 
E 4 HOH A 95 1195 82 HOH HOH . 
E 4 HOH A 96 1196 96 HOH HOH . 
E 4 HOH A 97 1197 127 HOH HOH . 
E 4 HOH A 98 1198 175 HOH HOH . 
E 4 HOH A 99 1199 50 HOH HOH . 
E 4 HOH A 100 1200 83 HOH HOH . 
E 4 HOH A 101 1201 167 HOH HOH . 
E 4 HOH A 102 1202 78 HOH HOH . 
E 4 HOH A 103 1203 113 HOH HOH . 
E 4 HOH A 104 1204 22 HOH HOH . 
E 4 HOH A 105 1205 75 HOH HOH . 
E 4 HOH A 106 1206 65 HOH HOH . 
E 4 HOH A 107 1207 5 HOH HOH . 
E 4 HOH A 108 1208 32 HOH HOH . 
E 4 HOH A 109 1209 106 HOH HOH . 
E 4 HOH A 110 1210 58 HOH HOH . 
E 4 HOH A 111 1211 131 HOH HOH . 
E 4 HOH A 112 1212 1 HOH HOH . 
E 4 HOH A 113 1213 119 HOH HOH . 
E 4 HOH A 114 1214 92 HOH HOH . 
E 4 HOH A 115 1215 153 HOH HOH . 
E 4 HOH A 116 1216 28 HOH HOH . 
E 4 HOH A 117 1217 66 HOH HOH . 
E 4 HOH A 118 1218 122 HOH HOH . 
E 4 HOH A 119 1219 88 HOH HOH . 
E 4 HOH A 120 1220 151 HOH HOH . 
E 4 HOH A 121 1221 9 HOH HOH . 
E 4 HOH A 122 1222 103 HOH HOH . 
E 4 HOH A 123 1223 99 HOH HOH . 
E 4 HOH A 124 1224 43 HOH HOH . 
E 4 HOH A 125 1225 111 HOH HOH . 
E 4 HOH A 126 1226 52 HOH HOH . 
E 4 HOH A 127 1227 29 HOH HOH . 
E 4 HOH A 128 1228 181 HOH HOH . 
E 4 HOH A 129 1229 18 HOH HOH . 
E 4 HOH A 130 1230 85 HOH HOH . 
E 4 HOH A 131 1231 74 HOH HOH . 
E 4 HOH A 132 1232 46 HOH HOH . 
E 4 HOH A 133 1233 67 HOH HOH . 
E 4 HOH A 134 1234 177 HOH HOH . 
E 4 HOH A 135 1235 90 HOH HOH . 
E 4 HOH A 136 1236 47 HOH HOH . 
E 4 HOH A 137 1237 152 HOH HOH . 
E 4 HOH A 138 1238 136 HOH HOH . 
E 4 HOH A 139 1239 134 HOH HOH . 
E 4 HOH A 140 1240 31 HOH HOH . 
E 4 HOH A 141 1241 141 HOH HOH . 
E 4 HOH A 142 1242 13 HOH HOH . 
E 4 HOH A 143 1243 4 HOH HOH . 
E 4 HOH A 144 1244 150 HOH HOH . 
E 4 HOH A 145 1245 157 HOH HOH . 
E 4 HOH A 146 1246 35 HOH HOH . 
E 4 HOH A 147 1247 180 HOH HOH . 
E 4 HOH A 148 1248 206 HOH HOH . 
E 4 HOH A 149 1249 214 HOH HOH . 
E 4 HOH A 150 1250 117 HOH HOH . 
E 4 HOH A 151 1251 187 HOH HOH . 
E 4 HOH A 152 1252 10 HOH HOH . 
E 4 HOH A 153 1253 170 HOH HOH . 
E 4 HOH A 154 1254 24 HOH HOH . 
E 4 HOH A 155 1255 69 HOH HOH . 
E 4 HOH A 156 1256 56 HOH HOH . 
E 4 HOH A 157 1257 156 HOH HOH . 
E 4 HOH A 158 1258 59 HOH HOH . 
E 4 HOH A 159 1259 169 HOH HOH . 
E 4 HOH A 160 1260 112 HOH HOH . 
E 4 HOH A 161 1261 215 HOH HOH . 
E 4 HOH A 162 1262 142 HOH HOH . 
E 4 HOH A 163 1263 196 HOH HOH . 
E 4 HOH A 164 1264 91 HOH HOH . 
E 4 HOH A 165 1265 198 HOH HOH . 
E 4 HOH A 166 1266 216 HOH HOH . 
E 4 HOH A 167 1267 120 HOH HOH . 
E 4 HOH A 168 1268 26 HOH HOH . 
E 4 HOH A 169 1269 145 HOH HOH . 
E 4 HOH A 170 1270 197 HOH HOH . 
E 4 HOH A 171 1271 200 HOH HOH . 
E 4 HOH A 172 1272 123 HOH HOH . 
E 4 HOH A 173 1273 223 HOH HOH . 
E 4 HOH A 174 1274 199 HOH HOH . 
E 4 HOH A 175 1275 72 HOH HOH . 
E 4 HOH A 176 1276 195 HOH HOH . 
E 4 HOH A 177 1277 147 HOH HOH . 
E 4 HOH A 178 1278 146 HOH HOH . 
E 4 HOH A 179 1279 25 HOH HOH . 
E 4 HOH A 180 1280 207 HOH HOH . 
E 4 HOH A 181 1281 51 HOH HOH . 
E 4 HOH A 182 1282 130 HOH HOH . 
E 4 HOH A 183 1283 104 HOH HOH . 
E 4 HOH A 184 1284 174 HOH HOH . 
E 4 HOH A 185 1285 39 HOH HOH . 
E 4 HOH A 186 1286 164 HOH HOH . 
E 4 HOH A 187 1287 125 HOH HOH . 
E 4 HOH A 188 1288 209 HOH HOH . 
E 4 HOH A 189 1289 89 HOH HOH . 
E 4 HOH A 190 1290 222 HOH HOH . 
E 4 HOH A 191 1291 191 HOH HOH . 
E 4 HOH A 192 1292 165 HOH HOH . 
E 4 HOH A 193 1293 30 HOH HOH . 
E 4 HOH A 194 1294 139 HOH HOH . 
E 4 HOH A 195 1295 107 HOH HOH . 
E 4 HOH A 196 1296 171 HOH HOH . 
E 4 HOH A 197 1297 42 HOH HOH . 
E 4 HOH A 198 1298 202 HOH HOH . 
E 4 HOH A 199 1299 33 HOH HOH . 
E 4 HOH A 200 1300 118 HOH HOH . 
E 4 HOH A 201 1301 217 HOH HOH . 
E 4 HOH A 202 1302 53 HOH HOH . 
E 4 HOH A 203 1303 203 HOH HOH . 
E 4 HOH A 204 1304 128 HOH HOH . 
E 4 HOH A 205 1305 138 HOH HOH . 
E 4 HOH A 206 1306 213 HOH HOH . 
E 4 HOH A 207 1307 135 HOH HOH . 
E 4 HOH A 208 1308 110 HOH HOH . 
E 4 HOH A 209 1309 210 HOH HOH . 
E 4 HOH A 210 1310 211 HOH HOH . 
E 4 HOH A 211 1311 219 HOH HOH . 
E 4 HOH A 212 1312 221 HOH HOH . 
E 4 HOH A 213 1313 220 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 MPD . . . C 3 32.229 -3.987 -29.989 1 19.87 ? C1 MPD 1002 A 1 
HETATM 2 C C2 MPD . . . C 3 32.957 -2.671 -29.769 1 16.94 ? C2 MPD 1002 A 1 
HETATM 3 O O2 MPD . . . C 3 34.069 -2.982 -28.913 1 20.96 ? O2 MPD 1002 A 1 
HETATM 4 C CM MPD . . . C 3 33.566 -2.144 -31.06 1 21.4 ? CM MPD 1002 A 1 
HETATM 5 C C3 MPD . . . C 3 32.012 -1.655 -29.074 1 17.42 ? C3 MPD 1002 A 1 
HETATM 6 C C4 MPD . . . C 3 32.582 -0.247 -28.895 1 16.5 ? C4 MPD 1002 A 1 
HETATM 7 O O4 MPD . . . C 3 31.763 0.652 -28.111 1 23.5 ? O4 MPD 1002 A 1 
HETATM 8 C C5 MPD . . . C 3 33.973 -0.328 -28.337 1 16.38 ? C5 MPD 1002 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           304 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           8 
#