data_3EK3
#
_model_server_result.job_id            VKCwzFR6_FKIpXCbOPfH1Q 
_model_server_result.datetime_utc      '2025-08-31 02:17:09' 
_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          3ek3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":203}' 
#
_entry.id    3EK3 
#
_exptl.entry_id    3EK3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.174 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4S)-2-METHYL-2,4-PENTANEDIOL 
_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         90 
_cell.entry_id            3EK3 
_cell.length_a            40.61 
_cell.length_b            83.73 
_cell.length_c            116.51 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3EK3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 3_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 58.255 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 D N N 
? 4 E N N 
? 4 F 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
covale ? covale1 A C GLY 43 A GLY 42 1_555 A N MSE 44 A MSE 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? 
covale ? covale2 A C MSE 44 A MSE 43 1_555 A N HIS 45 A HIS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? 
covale ? covale3 A C GLY 110 A GLY 109 1_555 A N MSE 111 A MSE 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? 
covale ? covale4 A C MSE 111 A MSE 110 1_555 A N ASP 112 A ASP 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
covale ? covale5 A C ASN 119 A ASN 118 1_555 A N MSE 120 A MSE 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? 
covale ? covale6 A C MSE 120 A MSE 119 1_555 A N PHE 121 A PHE 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? 
#
_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 272 n n 
C1 H11 MPD sing 273 n n 
C1 H12 MPD sing 274 n n 
C1 H13 MPD sing 275 n n 
C2 O2 MPD sing 276 n n 
C2 CM MPD sing 277 n n 
C2 C3 MPD sing 278 n n 
O2 HO2 MPD sing 279 n n 
CM HM1 MPD sing 280 n n 
CM HM2 MPD sing 281 n n 
CM HM3 MPD sing 282 n n 
C3 C4 MPD sing 283 n n 
C3 H31 MPD sing 284 n n 
C3 H32 MPD sing 285 n n 
C4 O4 MPD sing 286 n n 
C4 C5 MPD sing 287 n n 
C4 H4 MPD sing 288 n n 
O4 HO4 MPD sing 289 n n 
C5 H51 MPD sing 290 n n 
C5 H52 MPD sing 291 n n 
C5 H53 MPD sing 292 n n 
#
_atom_sites.entry_id                     3EK3 
_atom_sites.fract_transf_matrix[1][1]    0.024624 
_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]    0.011943 
_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]    0.008583 
_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 FMN A 1 200 200 FMN FMN . 
C 3 UNL A 1 201 201 UNL UNL . 
D 4 MPD A 1 202 202 MPD MPD . 
E 4 MPD A 1 203 203 MPD MPD . 
F 4 MPD A 1 204 204 MPD MPD . 
G 5 HOH A 1 205 205 HOH HOH . 
G 5 HOH A 2 206 206 HOH HOH . 
G 5 HOH A 3 207 207 HOH HOH . 
G 5 HOH A 4 208 208 HOH HOH . 
G 5 HOH A 5 209 209 HOH HOH . 
G 5 HOH A 6 210 210 HOH HOH . 
G 5 HOH A 7 211 211 HOH HOH . 
G 5 HOH A 8 212 212 HOH HOH . 
G 5 HOH A 9 213 213 HOH HOH . 
G 5 HOH A 10 214 214 HOH HOH . 
G 5 HOH A 11 215 215 HOH HOH . 
G 5 HOH A 12 216 216 HOH HOH . 
G 5 HOH A 13 217 217 HOH HOH . 
G 5 HOH A 14 218 218 HOH HOH . 
G 5 HOH A 15 219 219 HOH HOH . 
G 5 HOH A 16 220 220 HOH HOH . 
G 5 HOH A 17 221 221 HOH HOH . 
G 5 HOH A 18 222 222 HOH HOH . 
G 5 HOH A 19 223 223 HOH HOH . 
G 5 HOH A 20 224 224 HOH HOH . 
G 5 HOH A 21 225 225 HOH HOH . 
G 5 HOH A 22 226 226 HOH HOH . 
G 5 HOH A 23 227 227 HOH HOH . 
G 5 HOH A 24 228 228 HOH HOH . 
G 5 HOH A 25 229 229 HOH HOH . 
G 5 HOH A 26 230 230 HOH HOH . 
G 5 HOH A 27 231 231 HOH HOH . 
G 5 HOH A 28 232 232 HOH HOH . 
G 5 HOH A 29 233 233 HOH HOH . 
G 5 HOH A 30 234 234 HOH HOH . 
G 5 HOH A 31 235 235 HOH HOH . 
G 5 HOH A 32 236 236 HOH HOH . 
G 5 HOH A 33 237 237 HOH HOH . 
G 5 HOH A 34 238 238 HOH HOH . 
G 5 HOH A 35 239 239 HOH HOH . 
G 5 HOH A 36 240 240 HOH HOH . 
G 5 HOH A 37 241 241 HOH HOH . 
G 5 HOH A 38 242 242 HOH HOH . 
G 5 HOH A 39 243 243 HOH HOH . 
G 5 HOH A 40 244 244 HOH HOH . 
G 5 HOH A 41 245 245 HOH HOH . 
G 5 HOH A 42 246 246 HOH HOH . 
G 5 HOH A 43 247 247 HOH HOH . 
G 5 HOH A 44 248 248 HOH HOH . 
G 5 HOH A 45 249 249 HOH HOH . 
G 5 HOH A 46 250 250 HOH HOH . 
G 5 HOH A 47 251 251 HOH HOH . 
G 5 HOH A 48 252 252 HOH HOH . 
G 5 HOH A 49 253 253 HOH HOH . 
G 5 HOH A 50 254 254 HOH HOH . 
G 5 HOH A 51 255 255 HOH HOH . 
G 5 HOH A 52 256 256 HOH HOH . 
G 5 HOH A 53 257 257 HOH HOH . 
G 5 HOH A 54 258 258 HOH HOH . 
G 5 HOH A 55 259 259 HOH HOH . 
G 5 HOH A 56 260 260 HOH HOH . 
G 5 HOH A 57 261 261 HOH HOH . 
G 5 HOH A 58 262 262 HOH HOH . 
G 5 HOH A 59 263 263 HOH HOH . 
G 5 HOH A 60 264 264 HOH HOH . 
G 5 HOH A 61 265 265 HOH HOH . 
G 5 HOH A 62 266 266 HOH HOH . 
G 5 HOH A 63 267 267 HOH HOH . 
G 5 HOH A 64 268 268 HOH HOH . 
G 5 HOH A 65 269 269 HOH HOH . 
G 5 HOH A 66 270 270 HOH HOH . 
G 5 HOH A 67 271 271 HOH HOH . 
G 5 HOH A 68 272 272 HOH HOH . 
G 5 HOH A 69 273 273 HOH HOH . 
G 5 HOH A 70 274 274 HOH HOH . 
G 5 HOH A 71 275 275 HOH HOH . 
G 5 HOH A 72 276 276 HOH HOH . 
G 5 HOH A 73 277 277 HOH HOH . 
G 5 HOH A 74 278 278 HOH HOH . 
G 5 HOH A 75 279 279 HOH HOH . 
G 5 HOH A 76 280 280 HOH HOH . 
G 5 HOH A 77 281 281 HOH HOH . 
G 5 HOH A 78 282 282 HOH HOH . 
G 5 HOH A 79 283 283 HOH HOH . 
G 5 HOH A 80 284 284 HOH HOH . 
G 5 HOH A 81 285 285 HOH HOH . 
G 5 HOH A 82 286 286 HOH HOH . 
G 5 HOH A 83 287 287 HOH HOH . 
G 5 HOH A 84 288 288 HOH HOH . 
G 5 HOH A 85 289 289 HOH HOH . 
G 5 HOH A 86 290 290 HOH HOH . 
G 5 HOH A 87 291 291 HOH HOH . 
G 5 HOH A 88 292 292 HOH HOH . 
G 5 HOH A 89 293 293 HOH HOH . 
G 5 HOH A 90 294 294 HOH HOH . 
G 5 HOH A 91 295 295 HOH HOH . 
G 5 HOH A 92 296 296 HOH HOH . 
G 5 HOH A 93 297 297 HOH HOH . 
G 5 HOH A 94 298 298 HOH HOH . 
G 5 HOH A 95 299 299 HOH HOH . 
G 5 HOH A 96 300 300 HOH HOH . 
G 5 HOH A 97 301 301 HOH HOH . 
G 5 HOH A 98 302 302 HOH HOH . 
G 5 HOH A 99 303 303 HOH HOH . 
G 5 HOH A 100 304 304 HOH HOH . 
G 5 HOH A 101 305 305 HOH HOH . 
G 5 HOH A 102 306 306 HOH HOH . 
G 5 HOH A 103 307 307 HOH HOH . 
G 5 HOH A 104 308 308 HOH HOH . 
G 5 HOH A 105 309 309 HOH HOH . 
G 5 HOH A 106 310 310 HOH HOH . 
G 5 HOH A 107 311 311 HOH HOH . 
G 5 HOH A 108 312 312 HOH HOH . 
G 5 HOH A 109 313 313 HOH HOH . 
G 5 HOH A 110 314 314 HOH HOH . 
G 5 HOH A 111 315 315 HOH HOH . 
G 5 HOH A 112 316 316 HOH HOH . 
G 5 HOH A 113 317 317 HOH HOH . 
G 5 HOH A 114 318 318 HOH HOH . 
G 5 HOH A 115 319 319 HOH HOH . 
G 5 HOH A 116 320 320 HOH HOH . 
G 5 HOH A 117 321 321 HOH HOH . 
G 5 HOH A 118 322 322 HOH HOH . 
G 5 HOH A 119 323 323 HOH HOH . 
G 5 HOH A 120 324 324 HOH HOH . 
G 5 HOH A 121 325 325 HOH HOH . 
G 5 HOH A 122 326 326 HOH HOH . 
G 5 HOH A 123 327 327 HOH HOH . 
G 5 HOH A 124 328 328 HOH HOH . 
G 5 HOH A 125 329 329 HOH HOH . 
G 5 HOH A 126 330 330 HOH HOH . 
G 5 HOH A 127 331 331 HOH HOH . 
G 5 HOH A 128 332 332 HOH HOH . 
G 5 HOH A 129 333 333 HOH HOH . 
G 5 HOH A 130 334 334 HOH HOH . 
G 5 HOH A 131 335 335 HOH HOH . 
G 5 HOH A 132 336 336 HOH HOH . 
G 5 HOH A 133 337 337 HOH HOH . 
G 5 HOH A 134 338 338 HOH HOH . 
G 5 HOH A 135 339 339 HOH HOH . 
G 5 HOH A 136 340 340 HOH HOH . 
G 5 HOH A 137 341 341 HOH HOH . 
G 5 HOH A 138 342 342 HOH HOH . 
G 5 HOH A 139 343 343 HOH HOH . 
G 5 HOH A 140 344 344 HOH HOH . 
G 5 HOH A 141 345 345 HOH HOH . 
G 5 HOH A 142 346 346 HOH HOH . 
G 5 HOH A 143 347 347 HOH HOH . 
G 5 HOH A 144 348 348 HOH HOH . 
G 5 HOH A 145 349 349 HOH HOH . 
G 5 HOH A 146 350 350 HOH HOH . 
G 5 HOH A 147 351 351 HOH HOH . 
G 5 HOH A 148 352 352 HOH HOH . 
G 5 HOH A 149 353 353 HOH HOH . 
G 5 HOH A 150 354 354 HOH HOH . 
G 5 HOH A 151 355 355 HOH HOH . 
G 5 HOH A 152 356 356 HOH HOH . 
G 5 HOH A 153 357 357 HOH HOH . 
G 5 HOH A 154 358 358 HOH HOH . 
G 5 HOH A 155 359 359 HOH HOH . 
G 5 HOH A 156 360 360 HOH HOH . 
G 5 HOH A 157 361 361 HOH HOH . 
G 5 HOH A 158 362 362 HOH HOH . 
G 5 HOH A 159 363 363 HOH HOH . 
G 5 HOH A 160 364 364 HOH HOH . 
G 5 HOH A 161 365 365 HOH HOH . 
G 5 HOH A 162 366 366 HOH HOH . 
G 5 HOH A 163 367 367 HOH HOH . 
G 5 HOH A 164 368 368 HOH HOH . 
G 5 HOH A 165 369 369 HOH HOH . 
G 5 HOH A 166 370 370 HOH HOH . 
G 5 HOH A 167 371 371 HOH HOH . 
G 5 HOH A 168 372 372 HOH HOH . 
G 5 HOH A 169 373 373 HOH HOH . 
G 5 HOH A 170 374 374 HOH HOH . 
G 5 HOH A 171 375 375 HOH HOH . 
G 5 HOH A 172 376 376 HOH HOH . 
G 5 HOH A 173 377 377 HOH HOH . 
G 5 HOH A 174 378 378 HOH HOH . 
G 5 HOH A 175 379 379 HOH HOH . 
G 5 HOH A 176 380 380 HOH HOH . 
G 5 HOH A 177 381 381 HOH HOH . 
G 5 HOH A 178 382 382 HOH HOH . 
G 5 HOH A 179 383 383 HOH HOH . 
G 5 HOH A 180 384 384 HOH HOH . 
G 5 HOH A 181 385 385 HOH HOH . 
G 5 HOH A 182 386 386 HOH HOH . 
G 5 HOH A 183 387 387 HOH HOH . 
G 5 HOH A 184 388 388 HOH HOH . 
G 5 HOH A 185 389 389 HOH HOH . 
G 5 HOH A 186 390 390 HOH HOH . 
G 5 HOH A 187 391 391 HOH HOH . 
G 5 HOH A 188 392 392 HOH HOH . 
G 5 HOH A 189 393 393 HOH HOH . 
G 5 HOH A 190 394 394 HOH HOH . 
G 5 HOH A 191 395 395 HOH HOH . 
G 5 HOH A 192 396 396 HOH HOH . 
G 5 HOH A 193 397 397 HOH HOH . 
G 5 HOH A 194 398 398 HOH HOH . 
G 5 HOH A 195 399 399 HOH HOH . 
G 5 HOH A 196 400 400 HOH HOH . 
G 5 HOH A 197 401 401 HOH HOH . 
G 5 HOH A 198 402 402 HOH HOH . 
G 5 HOH A 199 403 403 HOH HOH . 
G 5 HOH A 200 404 404 HOH HOH . 
G 5 HOH A 201 405 405 HOH HOH . 
G 5 HOH A 202 406 406 HOH HOH . 
G 5 HOH A 203 407 407 HOH HOH . 
G 5 HOH A 204 408 408 HOH HOH . 
G 5 HOH A 205 409 409 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 . A . E 4 0.212 13.434 24.093 0.5 27.63 ? C1 MPD 203 A 1 
HETATM 2 C C1 MPD . B . E 4 -0.946 14.028 23.584 0.5 31.46 ? C1 MPD 203 A 1 
HETATM 3 C C2 MPD . A . E 4 0.018 13.404 22.579 0.5 31.02 ? C2 MPD 203 A 1 
HETATM 4 C C2 MPD . B . E 4 -0.046 13.717 22.396 0.5 29.82 ? C2 MPD 203 A 1 
HETATM 5 O O2 MPD . A . E 4 0.918 12.406 22.034 0.5 31.58 ? O2 MPD 203 A 1 
HETATM 6 O O2 MPD . B . E 4 0.504 12.4 22.649 0.5 40.11 ? O2 MPD 203 A 1 
HETATM 7 C CM MPD . A . E 4 -1.405 12.983 22.24 0.5 23.97 ? CM MPD 203 A 1 
HETATM 8 C CM MPD . B . E 4 -0.909 13.648 21.145 0.5 26.25 ? CM MPD 203 A 1 
HETATM 9 C C3 MPD . A . E 4 0.358 14.753 21.947 0.5 30.25 ? C3 MPD 203 A 1 
HETATM 10 C C3 MPD . B . E 4 1.072 14.77 22.262 0.5 30.96 ? C3 MPD 203 A 1 
HETATM 11 C C4 MPD . A . E 4 1.862 15.046 21.836 0.5 30.81 ? C4 MPD 203 A 1 
HETATM 12 C C4 MPD . B . E 4 2.484 14.288 21.886 0.5 29.51 ? C4 MPD 203 A 1 
HETATM 13 O O4 MPD . A . E 4 2.103 16.432 21.673 0.5 22.37 ? O4 MPD 203 A 1 
HETATM 14 O O4 MPD . B . E 4 2.79 14.55 20.523 0.5 27.89 ? O4 MPD 203 A 1 
HETATM 15 C C5 MPD . A . E 4 2.648 14.611 23.057 0.5 26.92 ? C5 MPD 203 A 1 
HETATM 16 C C5 MPD . B . E 4 3.523 15.008 22.731 0.5 20.66 ? C5 MPD 203 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           293 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           16 
#