data_2PNZ
#
_model_server_result.job_id            AwzcfXc5IPJwVXzWBgLtJQ 
_model_server_result.datetime_utc      '2024-11-26 23:18:29' 
_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          2pnz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":251}' 
#
_entry.id    2PNZ 
#
_exptl.entry_id    2PNZ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.174 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4S)-2-METHYL-2,4-PENTANEDIOL 
_entity.pdbx_number_of_molecules    5 
_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            2PNZ 
_cell.length_a            93.81 
_cell.length_b            93.81 
_cell.length_c            126.26 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2PNZ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        150 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 3 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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    1,2,3 
#
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' 2_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -46.905 81.241843 0 
3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -93.81 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 5 E N N 
? 5 F N N 
? 5 G N N 
? 5 H N N 
? 5 I N N 
#
_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 277 n n 
C1 H11 MPD sing 278 n n 
C1 H12 MPD sing 279 n n 
C1 H13 MPD sing 280 n n 
C2 O2 MPD sing 281 n n 
C2 CM MPD sing 282 n n 
C2 C3 MPD sing 283 n n 
O2 HO2 MPD sing 284 n n 
CM HM1 MPD sing 285 n n 
CM HM2 MPD sing 286 n n 
CM HM3 MPD sing 287 n n 
C3 C4 MPD sing 288 n n 
C3 H31 MPD sing 289 n n 
C3 H32 MPD sing 290 n n 
C4 O4 MPD sing 291 n n 
C4 C5 MPD sing 292 n n 
C4 H4 MPD sing 293 n n 
O4 HO4 MPD sing 294 n n 
C5 H51 MPD sing 295 n n 
C5 H52 MPD sing 296 n n 
C5 H53 MPD sing 297 n n 
#
_atom_sites.entry_id                     2PNZ 
_atom_sites.fract_transf_matrix[1][1]    0.01066 
_atom_sites.fract_transf_matrix[1][2]    0.006154 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012309 
_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]    0.00792 
_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 UDP A 1 250 250 UDP UDP . 
D 4 5GP A 1 279 279 5GP 5GP . 
E 5 MPD A 1 251 251 MPD MPD . 
F 5 MPD A 1 252 252 MPD MPD . 
G 5 MPD A 1 282 282 MPD MPD . 
H 5 MPD B 1 280 280 MPD MPD . 
I 5 MPD B 1 281 281 MPD MPD . 
J 6 HOH A 1 283 5 HOH HOH . 
J 6 HOH A 2 284 8 HOH HOH . 
J 6 HOH A 3 285 12 HOH HOH . 
J 6 HOH A 4 286 16 HOH HOH . 
J 6 HOH A 5 287 18 HOH HOH . 
J 6 HOH A 6 288 19 HOH HOH . 
J 6 HOH A 7 289 20 HOH HOH . 
J 6 HOH A 8 290 23 HOH HOH . 
J 6 HOH A 9 291 25 HOH HOH . 
J 6 HOH A 10 292 32 HOH HOH . 
J 6 HOH A 11 293 37 HOH HOH . 
J 6 HOH A 12 294 44 HOH HOH . 
J 6 HOH A 13 295 45 HOH HOH . 
J 6 HOH A 14 296 49 HOH HOH . 
J 6 HOH A 15 297 53 HOH HOH . 
J 6 HOH A 16 298 54 HOH HOH . 
J 6 HOH A 17 299 55 HOH HOH . 
J 6 HOH A 18 300 57 HOH HOH . 
J 6 HOH A 19 301 63 HOH HOH . 
J 6 HOH A 20 302 65 HOH HOH . 
J 6 HOH A 21 303 67 HOH HOH . 
J 6 HOH A 22 304 69 HOH HOH . 
J 6 HOH A 23 305 70 HOH HOH . 
J 6 HOH A 24 306 73 HOH HOH . 
J 6 HOH A 25 307 76 HOH HOH . 
J 6 HOH A 26 308 77 HOH HOH . 
J 6 HOH A 27 309 79 HOH HOH . 
J 6 HOH A 28 310 81 HOH HOH . 
J 6 HOH A 29 311 83 HOH HOH . 
J 6 HOH A 30 312 84 HOH HOH . 
J 6 HOH A 31 313 85 HOH HOH . 
J 6 HOH A 32 314 86 HOH HOH . 
J 6 HOH A 33 315 87 HOH HOH . 
J 6 HOH A 34 316 91 HOH HOH . 
J 6 HOH A 35 317 93 HOH HOH . 
J 6 HOH A 36 318 95 HOH HOH . 
J 6 HOH A 37 319 96 HOH HOH . 
J 6 HOH A 38 320 99 HOH HOH . 
J 6 HOH A 39 321 101 HOH HOH . 
J 6 HOH A 40 322 102 HOH HOH . 
J 6 HOH A 41 323 104 HOH HOH . 
J 6 HOH A 42 324 106 HOH HOH . 
J 6 HOH A 43 325 110 HOH HOH . 
J 6 HOH A 44 326 112 HOH HOH . 
J 6 HOH A 45 327 115 HOH HOH . 
J 6 HOH A 46 328 117 HOH HOH . 
J 6 HOH A 47 329 123 HOH HOH . 
J 6 HOH A 48 330 125 HOH HOH . 
J 6 HOH A 49 331 126 HOH HOH . 
J 6 HOH A 50 332 127 HOH HOH . 
J 6 HOH A 51 333 128 HOH HOH . 
J 6 HOH A 52 334 129 HOH HOH . 
J 6 HOH A 53 335 130 HOH HOH . 
J 6 HOH A 54 336 134 HOH HOH . 
J 6 HOH A 55 337 135 HOH HOH . 
J 6 HOH A 56 338 138 HOH HOH . 
J 6 HOH A 57 339 148 HOH HOH . 
J 6 HOH A 58 340 150 HOH HOH . 
J 6 HOH A 59 341 152 HOH HOH . 
J 6 HOH A 60 342 154 HOH HOH . 
J 6 HOH A 61 343 155 HOH HOH . 
J 6 HOH A 62 344 157 HOH HOH . 
J 6 HOH A 63 345 159 HOH HOH . 
J 6 HOH A 64 346 164 HOH HOH . 
J 6 HOH A 65 347 170 HOH HOH . 
J 6 HOH A 66 348 171 HOH HOH . 
J 6 HOH A 67 349 175 HOH HOH . 
J 6 HOH A 68 350 178 HOH HOH . 
J 6 HOH A 69 351 181 HOH HOH . 
J 6 HOH A 70 352 182 HOH HOH . 
J 6 HOH A 71 353 183 HOH HOH . 
J 6 HOH A 72 354 185 HOH HOH . 
J 6 HOH A 73 355 189 HOH HOH . 
J 6 HOH A 74 356 194 HOH HOH . 
J 6 HOH A 75 357 195 HOH HOH . 
J 6 HOH A 76 358 196 HOH HOH . 
J 6 HOH A 77 359 198 HOH HOH . 
J 6 HOH A 78 360 199 HOH HOH . 
J 6 HOH A 79 361 200 HOH HOH . 
J 6 HOH A 80 362 201 HOH HOH . 
J 6 HOH A 81 363 202 HOH HOH . 
J 6 HOH A 82 364 203 HOH HOH . 
J 6 HOH A 83 365 204 HOH HOH . 
J 6 HOH A 84 366 205 HOH HOH . 
J 6 HOH A 85 367 206 HOH HOH . 
J 6 HOH A 86 368 216 HOH HOH . 
J 6 HOH A 87 369 219 HOH HOH . 
J 6 HOH A 88 370 220 HOH HOH . 
J 6 HOH A 89 371 222 HOH HOH . 
J 6 HOH A 90 372 223 HOH HOH . 
J 6 HOH A 91 373 224 HOH HOH . 
J 6 HOH A 92 374 225 HOH HOH . 
J 6 HOH A 93 375 226 HOH HOH . 
J 6 HOH A 94 376 228 HOH HOH . 
J 6 HOH A 95 377 233 HOH HOH . 
J 6 HOH A 96 378 234 HOH HOH . 
J 6 HOH A 97 379 235 HOH HOH . 
J 6 HOH A 98 380 236 HOH HOH . 
J 6 HOH A 99 381 237 HOH HOH . 
J 6 HOH A 100 382 238 HOH HOH . 
K 6 HOH B 1 282 1 HOH HOH . 
K 6 HOH B 2 283 2 HOH HOH . 
K 6 HOH B 3 284 3 HOH HOH . 
K 6 HOH B 4 285 4 HOH HOH . 
K 6 HOH B 5 286 6 HOH HOH . 
K 6 HOH B 6 287 7 HOH HOH . 
K 6 HOH B 7 288 9 HOH HOH . 
K 6 HOH B 8 289 10 HOH HOH . 
K 6 HOH B 9 290 11 HOH HOH . 
K 6 HOH B 10 291 13 HOH HOH . 
K 6 HOH B 11 292 14 HOH HOH . 
K 6 HOH B 12 293 15 HOH HOH . 
K 6 HOH B 13 294 17 HOH HOH . 
K 6 HOH B 14 295 21 HOH HOH . 
K 6 HOH B 15 296 22 HOH HOH . 
K 6 HOH B 16 297 24 HOH HOH . 
K 6 HOH B 17 298 26 HOH HOH . 
K 6 HOH B 18 299 27 HOH HOH . 
K 6 HOH B 19 300 28 HOH HOH . 
K 6 HOH B 20 301 29 HOH HOH . 
K 6 HOH B 21 302 30 HOH HOH . 
K 6 HOH B 22 303 31 HOH HOH . 
K 6 HOH B 23 304 33 HOH HOH . 
K 6 HOH B 24 305 34 HOH HOH . 
K 6 HOH B 25 306 35 HOH HOH . 
K 6 HOH B 26 307 36 HOH HOH . 
K 6 HOH B 27 308 38 HOH HOH . 
K 6 HOH B 28 309 39 HOH HOH . 
K 6 HOH B 29 310 40 HOH HOH . 
K 6 HOH B 30 311 41 HOH HOH . 
K 6 HOH B 31 312 42 HOH HOH . 
K 6 HOH B 32 313 43 HOH HOH . 
K 6 HOH B 33 314 46 HOH HOH . 
K 6 HOH B 34 315 47 HOH HOH . 
K 6 HOH B 35 316 48 HOH HOH . 
K 6 HOH B 36 317 50 HOH HOH . 
K 6 HOH B 37 318 51 HOH HOH . 
K 6 HOH B 38 319 52 HOH HOH . 
K 6 HOH B 39 320 56 HOH HOH . 
K 6 HOH B 40 321 58 HOH HOH . 
K 6 HOH B 41 322 59 HOH HOH . 
K 6 HOH B 42 323 60 HOH HOH . 
K 6 HOH B 43 324 61 HOH HOH . 
K 6 HOH B 44 325 62 HOH HOH . 
K 6 HOH B 45 326 64 HOH HOH . 
K 6 HOH B 46 327 66 HOH HOH . 
K 6 HOH B 47 328 68 HOH HOH . 
K 6 HOH B 48 329 71 HOH HOH . 
K 6 HOH B 49 330 72 HOH HOH . 
K 6 HOH B 50 331 74 HOH HOH . 
K 6 HOH B 51 332 75 HOH HOH . 
K 6 HOH B 52 333 78 HOH HOH . 
K 6 HOH B 53 334 80 HOH HOH . 
K 6 HOH B 54 335 88 HOH HOH . 
K 6 HOH B 55 336 89 HOH HOH . 
K 6 HOH B 56 337 90 HOH HOH . 
K 6 HOH B 57 338 92 HOH HOH . 
K 6 HOH B 58 339 94 HOH HOH . 
K 6 HOH B 59 340 97 HOH HOH . 
K 6 HOH B 60 341 98 HOH HOH . 
K 6 HOH B 61 342 100 HOH HOH . 
K 6 HOH B 62 343 103 HOH HOH . 
K 6 HOH B 63 344 105 HOH HOH . 
K 6 HOH B 64 345 107 HOH HOH . 
K 6 HOH B 65 346 108 HOH HOH . 
K 6 HOH B 66 347 109 HOH HOH . 
K 6 HOH B 67 348 111 HOH HOH . 
K 6 HOH B 68 349 113 HOH HOH . 
K 6 HOH B 69 350 114 HOH HOH . 
K 6 HOH B 70 351 116 HOH HOH . 
K 6 HOH B 71 352 118 HOH HOH . 
K 6 HOH B 72 353 119 HOH HOH . 
K 6 HOH B 73 354 120 HOH HOH . 
K 6 HOH B 74 355 121 HOH HOH . 
K 6 HOH B 75 356 122 HOH HOH . 
K 6 HOH B 76 357 124 HOH HOH . 
K 6 HOH B 77 358 132 HOH HOH . 
K 6 HOH B 78 359 133 HOH HOH . 
K 6 HOH B 79 360 136 HOH HOH . 
K 6 HOH B 80 361 137 HOH HOH . 
K 6 HOH B 81 362 139 HOH HOH . 
K 6 HOH B 82 363 140 HOH HOH . 
K 6 HOH B 83 364 141 HOH HOH . 
K 6 HOH B 84 365 142 HOH HOH . 
K 6 HOH B 85 366 143 HOH HOH . 
K 6 HOH B 86 367 144 HOH HOH . 
K 6 HOH B 87 368 145 HOH HOH . 
K 6 HOH B 88 369 146 HOH HOH . 
K 6 HOH B 89 370 147 HOH HOH . 
K 6 HOH B 90 371 149 HOH HOH . 
K 6 HOH B 91 372 151 HOH HOH . 
K 6 HOH B 92 373 153 HOH HOH . 
K 6 HOH B 93 374 156 HOH HOH . 
K 6 HOH B 94 375 158 HOH HOH . 
K 6 HOH B 95 376 160 HOH HOH . 
K 6 HOH B 96 377 161 HOH HOH . 
K 6 HOH B 97 378 162 HOH HOH . 
K 6 HOH B 98 379 163 HOH HOH . 
K 6 HOH B 99 380 165 HOH HOH . 
K 6 HOH B 100 381 166 HOH HOH . 
K 6 HOH B 101 382 167 HOH HOH . 
K 6 HOH B 102 383 168 HOH HOH . 
K 6 HOH B 103 384 169 HOH HOH . 
K 6 HOH B 104 385 172 HOH HOH . 
K 6 HOH B 105 386 173 HOH HOH . 
K 6 HOH B 106 387 174 HOH HOH . 
K 6 HOH B 107 388 176 HOH HOH . 
K 6 HOH B 108 389 177 HOH HOH . 
K 6 HOH B 109 390 179 HOH HOH . 
K 6 HOH B 110 391 180 HOH HOH . 
K 6 HOH B 111 392 184 HOH HOH . 
K 6 HOH B 112 393 186 HOH HOH . 
K 6 HOH B 113 394 187 HOH HOH . 
K 6 HOH B 114 395 188 HOH HOH . 
K 6 HOH B 115 396 190 HOH HOH . 
K 6 HOH B 116 397 191 HOH HOH . 
K 6 HOH B 117 398 192 HOH HOH . 
K 6 HOH B 118 399 193 HOH HOH . 
K 6 HOH B 119 400 197 HOH HOH . 
K 6 HOH B 120 401 207 HOH HOH . 
K 6 HOH B 121 402 208 HOH HOH . 
K 6 HOH B 122 403 209 HOH HOH . 
K 6 HOH B 123 404 210 HOH HOH . 
K 6 HOH B 124 405 211 HOH HOH . 
K 6 HOH B 125 406 212 HOH HOH . 
K 6 HOH B 126 407 213 HOH HOH . 
K 6 HOH B 127 408 214 HOH HOH . 
K 6 HOH B 128 409 215 HOH HOH . 
K 6 HOH B 129 410 217 HOH HOH . 
K 6 HOH B 130 411 218 HOH HOH . 
K 6 HOH B 131 412 221 HOH HOH . 
K 6 HOH B 132 413 227 HOH HOH . 
K 6 HOH B 133 414 229 HOH HOH . 
K 6 HOH B 134 415 230 HOH HOH . 
K 6 HOH B 135 416 231 HOH HOH . 
K 6 HOH B 136 417 232 HOH HOH . 
K 6 HOH B 137 418 239 HOH HOH . 
K 6 HOH B 138 419 240 HOH HOH . 
K 6 HOH B 139 420 241 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 . . . E 5 -23.814 10.339 -20.579 1 51.59 ? C1 MPD 251 A 1 
HETATM 2 C C2 MPD . . . E 5 -23.24 10.798 -21.925 1 50.99 ? C2 MPD 251 A 1 
HETATM 3 O O2 MPD . . . E 5 -22.691 9.623 -22.639 1 44.31 ? O2 MPD 251 A 1 
HETATM 4 C CM MPD . . . E 5 -22.196 11.876 -21.604 1 47.45 ? CM MPD 251 A 1 
HETATM 5 C C3 MPD . . . E 5 -24.29 11.458 -22.807 1 50.33 ? C3 MPD 251 A 1 
HETATM 6 C C4 MPD . . . E 5 -25.736 11.377 -22.317 1 53.81 ? C4 MPD 251 A 1 
HETATM 7 O O4 MPD . . . E 5 -25.92 11.802 -20.969 1 54.06 ? O4 MPD 251 A 1 
HETATM 8 C C5 MPD . . . E 5 -26.569 12.26 -23.243 1 56.37 ? C5 MPD 251 A 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           8 
#