data_2DKV
#
_model_server_result.job_id            WsUFv9BGWSsYs6-dQooB0g 
_model_server_result.datetime_utc      '2024-10-19 16:46:19' 
_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          2dkv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":343}' 
#
_entry.id    2DKV 
#
_exptl.entry_id    2DKV 
_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            2DKV 
_cell.length_a            66.452 
_cell.length_b            66.452 
_cell.length_c            123.636 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2DKV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 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 
_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 D N N 
? 3 E 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 4 A CYS 35 1_555 A SG CYS 19 A CYS 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf2 A SG CYS 13 A CYS 44 1_555 A SG CYS 25 A CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf3 A SG CYS 16 A CYS 47 1_555 A SG CYS 43 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
disulf ? disulf4 A SG CYS 18 A CYS 49 1_555 A SG CYS 32 A CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? 
disulf ? disulf5 A SG CYS 36 A CYS 67 1_555 A SG CYS 40 A CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf6 A SG CYS 79 A CYS 110 1_555 A SG CYS 141 A CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? 
disulf ? disulf7 A SG CYS 153 A CYS 184 1_555 A SG CYS 161 A CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf8 A SG CYS 260 A CYS 291 1_555 A SG CYS 292 A CYS 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
#
_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 262 n n 
C1 H11 MPD sing 263 n n 
C1 H12 MPD sing 264 n n 
C1 H13 MPD sing 265 n n 
C2 O2 MPD sing 266 n n 
C2 CM MPD sing 267 n n 
C2 C3 MPD sing 268 n n 
O2 HO2 MPD sing 269 n n 
CM HM1 MPD sing 270 n n 
CM HM2 MPD sing 271 n n 
CM HM3 MPD sing 272 n n 
C3 C4 MPD sing 273 n n 
C3 H31 MPD sing 274 n n 
C3 H32 MPD sing 275 n n 
C4 O4 MPD sing 276 n n 
C4 C5 MPD sing 277 n n 
C4 H4 MPD sing 278 n n 
O4 HO4 MPD sing 279 n n 
C5 H51 MPD sing 280 n n 
C5 H52 MPD sing 281 n n 
C5 H53 MPD sing 282 n n 
#
_atom_sites.entry_id                     2DKV 
_atom_sites.fract_transf_matrix[1][1]    0.015049 
_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]    0.015049 
_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]    0.008088 
_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 MES A 1 341 1 MES MES . 
C 2 MES A 1 342 2 MES MES . 
D 3 MPD A 1 343 1 MPD MPD . 
E 3 MPD A 1 344 2 MPD MPD . 
F 4 HOH A 1 345 1 HOH HOH . 
F 4 HOH A 2 346 2 HOH HOH . 
F 4 HOH A 3 347 3 HOH HOH . 
F 4 HOH A 4 348 4 HOH HOH . 
F 4 HOH A 5 349 5 HOH HOH . 
F 4 HOH A 6 350 6 HOH HOH . 
F 4 HOH A 7 351 7 HOH HOH . 
F 4 HOH A 8 352 8 HOH HOH . 
F 4 HOH A 9 353 9 HOH HOH . 
F 4 HOH A 10 354 10 HOH HOH . 
F 4 HOH A 11 355 11 HOH HOH . 
F 4 HOH A 12 356 12 HOH HOH . 
F 4 HOH A 13 357 13 HOH HOH . 
F 4 HOH A 14 358 14 HOH HOH . 
F 4 HOH A 15 359 15 HOH HOH . 
F 4 HOH A 16 360 16 HOH HOH . 
F 4 HOH A 17 361 17 HOH HOH . 
F 4 HOH A 18 362 18 HOH HOH . 
F 4 HOH A 19 363 19 HOH HOH . 
F 4 HOH A 20 364 20 HOH HOH . 
F 4 HOH A 21 365 21 HOH HOH . 
F 4 HOH A 22 366 22 HOH HOH . 
F 4 HOH A 23 367 23 HOH HOH . 
F 4 HOH A 24 368 24 HOH HOH . 
F 4 HOH A 25 369 25 HOH HOH . 
F 4 HOH A 26 370 26 HOH HOH . 
F 4 HOH A 27 371 27 HOH HOH . 
F 4 HOH A 28 372 28 HOH HOH . 
F 4 HOH A 29 373 29 HOH HOH . 
F 4 HOH A 30 374 30 HOH HOH . 
F 4 HOH A 31 375 31 HOH HOH . 
F 4 HOH A 32 376 32 HOH HOH . 
F 4 HOH A 33 377 33 HOH HOH . 
F 4 HOH A 34 378 34 HOH HOH . 
F 4 HOH A 35 379 35 HOH HOH . 
F 4 HOH A 36 380 36 HOH HOH . 
F 4 HOH A 37 381 37 HOH HOH . 
F 4 HOH A 38 382 38 HOH HOH . 
F 4 HOH A 39 383 39 HOH HOH . 
F 4 HOH A 40 384 40 HOH HOH . 
F 4 HOH A 41 385 41 HOH HOH . 
F 4 HOH A 42 386 42 HOH HOH . 
F 4 HOH A 43 387 43 HOH HOH . 
F 4 HOH A 44 388 44 HOH HOH . 
F 4 HOH A 45 389 45 HOH HOH . 
F 4 HOH A 46 390 46 HOH HOH . 
F 4 HOH A 47 391 47 HOH HOH . 
F 4 HOH A 48 392 48 HOH HOH . 
F 4 HOH A 49 393 49 HOH HOH . 
F 4 HOH A 50 394 50 HOH HOH . 
F 4 HOH A 51 395 51 HOH HOH . 
F 4 HOH A 52 396 52 HOH HOH . 
F 4 HOH A 53 397 53 HOH HOH . 
F 4 HOH A 54 398 54 HOH HOH . 
F 4 HOH A 55 399 55 HOH HOH . 
F 4 HOH A 56 400 56 HOH HOH . 
F 4 HOH A 57 401 57 HOH HOH . 
F 4 HOH A 58 402 58 HOH HOH . 
F 4 HOH A 59 403 59 HOH HOH . 
F 4 HOH A 60 404 60 HOH HOH . 
F 4 HOH A 61 405 61 HOH HOH . 
F 4 HOH A 62 406 62 HOH HOH . 
F 4 HOH A 63 407 63 HOH HOH . 
F 4 HOH A 64 408 64 HOH HOH . 
F 4 HOH A 65 409 65 HOH HOH . 
F 4 HOH A 66 410 66 HOH HOH . 
F 4 HOH A 67 411 67 HOH HOH . 
F 4 HOH A 68 412 68 HOH HOH . 
F 4 HOH A 69 413 69 HOH HOH . 
F 4 HOH A 70 414 70 HOH HOH . 
F 4 HOH A 71 415 71 HOH HOH . 
F 4 HOH A 72 416 72 HOH HOH . 
F 4 HOH A 73 417 73 HOH HOH . 
F 4 HOH A 74 418 74 HOH HOH . 
F 4 HOH A 75 419 75 HOH HOH . 
F 4 HOH A 76 420 76 HOH HOH . 
F 4 HOH A 77 421 77 HOH HOH . 
F 4 HOH A 78 422 78 HOH HOH . 
F 4 HOH A 79 423 79 HOH HOH . 
F 4 HOH A 80 424 80 HOH HOH . 
F 4 HOH A 81 425 81 HOH HOH . 
F 4 HOH A 82 426 82 HOH HOH . 
F 4 HOH A 83 427 83 HOH HOH . 
F 4 HOH A 84 428 84 HOH HOH . 
F 4 HOH A 85 429 85 HOH HOH . 
F 4 HOH A 86 430 86 HOH HOH . 
F 4 HOH A 87 431 87 HOH HOH . 
F 4 HOH A 88 432 88 HOH HOH . 
F 4 HOH A 89 433 89 HOH HOH . 
F 4 HOH A 90 434 90 HOH HOH . 
F 4 HOH A 91 435 91 HOH HOH . 
F 4 HOH A 92 436 92 HOH HOH . 
F 4 HOH A 93 437 93 HOH HOH . 
F 4 HOH A 94 438 94 HOH HOH . 
F 4 HOH A 95 439 95 HOH HOH . 
F 4 HOH A 96 440 96 HOH HOH . 
F 4 HOH A 97 441 97 HOH HOH . 
F 4 HOH A 98 442 98 HOH HOH . 
F 4 HOH A 99 443 99 HOH HOH . 
F 4 HOH A 100 444 100 HOH HOH . 
F 4 HOH A 101 445 101 HOH HOH . 
F 4 HOH A 102 446 102 HOH HOH . 
F 4 HOH A 103 447 103 HOH HOH . 
F 4 HOH A 104 448 104 HOH HOH . 
F 4 HOH A 105 449 105 HOH HOH . 
F 4 HOH A 106 450 106 HOH HOH . 
F 4 HOH A 107 451 107 HOH HOH . 
F 4 HOH A 108 452 108 HOH HOH . 
F 4 HOH A 109 453 109 HOH HOH . 
F 4 HOH A 110 454 110 HOH HOH . 
F 4 HOH A 111 455 111 HOH HOH . 
F 4 HOH A 112 456 112 HOH HOH . 
F 4 HOH A 113 457 113 HOH HOH . 
F 4 HOH A 114 458 114 HOH HOH . 
F 4 HOH A 115 459 115 HOH HOH . 
F 4 HOH A 116 460 116 HOH HOH . 
F 4 HOH A 117 461 117 HOH HOH . 
F 4 HOH A 118 462 118 HOH HOH . 
F 4 HOH A 119 463 119 HOH HOH . 
F 4 HOH A 120 464 120 HOH HOH . 
F 4 HOH A 121 465 121 HOH HOH . 
F 4 HOH A 122 466 122 HOH HOH . 
F 4 HOH A 123 467 123 HOH HOH . 
F 4 HOH A 124 468 124 HOH HOH . 
F 4 HOH A 125 469 125 HOH HOH . 
F 4 HOH A 126 470 126 HOH HOH . 
F 4 HOH A 127 471 127 HOH HOH . 
F 4 HOH A 128 472 128 HOH HOH . 
F 4 HOH A 129 473 129 HOH HOH . 
F 4 HOH A 130 474 130 HOH HOH . 
F 4 HOH A 131 475 131 HOH HOH . 
F 4 HOH A 132 476 132 HOH HOH . 
F 4 HOH A 133 477 133 HOH HOH . 
F 4 HOH A 134 478 134 HOH HOH . 
F 4 HOH A 135 479 135 HOH HOH . 
F 4 HOH A 136 480 136 HOH HOH . 
F 4 HOH A 137 481 137 HOH HOH . 
F 4 HOH A 138 482 138 HOH HOH . 
F 4 HOH A 139 483 139 HOH HOH . 
F 4 HOH A 140 484 140 HOH HOH . 
F 4 HOH A 141 485 141 HOH HOH . 
F 4 HOH A 142 486 142 HOH HOH . 
F 4 HOH A 143 487 143 HOH HOH . 
F 4 HOH A 144 488 144 HOH HOH . 
F 4 HOH A 145 489 145 HOH HOH . 
F 4 HOH A 146 490 146 HOH HOH . 
F 4 HOH A 147 491 147 HOH HOH . 
F 4 HOH A 148 492 148 HOH HOH . 
F 4 HOH A 149 493 149 HOH HOH . 
F 4 HOH A 150 494 150 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 . . . D 3 22.308 15.455 26.78 1 53.65 ? C1 MPD 343 A 1 
HETATM 2 C C2 MPD . . . D 3 21.265 16.575 26.593 1 54.52 ? C2 MPD 343 A 1 
HETATM 3 O O2 MPD . . . D 3 19.97 16.125 27.093 1 51.44 ? O2 MPD 343 A 1 
HETATM 4 C CM MPD . . . D 3 21.646 17.863 27.33 1 55.11 ? CM MPD 343 A 1 
HETATM 5 C C3 MPD . . . D 3 21.08 16.892 25.109 1 54.59 ? C3 MPD 343 A 1 
HETATM 6 C C4 MPD . . . D 3 22.343 17.39 24.393 1 54.48 ? C4 MPD 343 A 1 
HETATM 7 O O4 MPD . . . D 3 22.843 16.405 23.497 1 53.48 ? O4 MPD 343 A 1 
HETATM 8 C C5 MPD . . . D 3 22.058 18.685 23.625 1 54.75 ? C5 MPD 343 A 1 
#
_model_server_stats.io_time_ms              48 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           299 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           8 
#