data_4YXM # _model_server_result.job_id 9ghuxsu_mNeyYKoQrfeNWw _model_server_result.datetime_utc '2024-11-19 10:34:01' _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 4yxm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 4YXM # _exptl.entry_id 4YXM _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 1 _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 4YXM _cell.length_a 108.55 _cell.length_b 108.55 _cell.length_c 165.92 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YXM _symmetry.cell_setting ? _symmetry.Int_Tables_number 90 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 4 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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 1,2,3,4 # 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_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -108.55 0 3 'crystal symmetry operation' 3_445 -y-1/2,x-1/2,z 0 -1 0 1 0 0 0 0 1 -54.275 -54.275 0 4 'crystal symmetry operation' 4_545 y+1/2,-x-1/2,z 0 1 0 -1 0 0 0 0 1 54.275 -54.275 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 298 n n C1 H11 MPD sing 299 n n C1 H12 MPD sing 300 n n C1 H13 MPD sing 301 n n C2 O2 MPD sing 302 n n C2 CM MPD sing 303 n n C2 C3 MPD sing 304 n n O2 HO2 MPD sing 305 n n CM HM1 MPD sing 306 n n CM HM2 MPD sing 307 n n CM HM3 MPD sing 308 n n C3 C4 MPD sing 309 n n C3 H31 MPD sing 310 n n C3 H32 MPD sing 311 n n C4 O4 MPD sing 312 n n C4 C5 MPD sing 313 n n C4 H4 MPD sing 314 n n O4 HO4 MPD sing 315 n n C5 H51 MPD sing 316 n n C5 H52 MPD sing 317 n n C5 H53 MPD sing 318 n n # _atom_sites.entry_id 4YXM _atom_sites.fract_transf_matrix[1][1] 0.009212 _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] 0.009212 _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] 0.006027 _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 2 2BA B 1 401 1 2BA 2BA . D 3 MPD B 1 402 1 MPD MPD . E 4 HOH A 1 401 67 HOH HOH . E 4 HOH A 2 402 72 HOH HOH . E 4 HOH A 3 403 33 HOH HOH . E 4 HOH A 4 404 133 HOH HOH . E 4 HOH A 5 405 139 HOH HOH . E 4 HOH A 6 406 134 HOH HOH . E 4 HOH A 7 407 77 HOH HOH . E 4 HOH A 8 408 34 HOH HOH . E 4 HOH A 9 409 112 HOH HOH . E 4 HOH A 10 410 22 HOH HOH . E 4 HOH A 11 411 59 HOH HOH . E 4 HOH A 12 412 20 HOH HOH . E 4 HOH A 13 413 16 HOH HOH . E 4 HOH A 14 414 45 HOH HOH . E 4 HOH A 15 415 40 HOH HOH . E 4 HOH A 16 416 36 HOH HOH . E 4 HOH A 17 417 51 HOH HOH . E 4 HOH A 18 418 10 HOH HOH . E 4 HOH A 19 419 30 HOH HOH . E 4 HOH A 20 420 26 HOH HOH . E 4 HOH A 21 421 88 HOH HOH . E 4 HOH A 22 422 37 HOH HOH . E 4 HOH A 23 423 62 HOH HOH . E 4 HOH A 24 424 14 HOH HOH . E 4 HOH A 25 425 6 HOH HOH . E 4 HOH A 26 426 11 HOH HOH . E 4 HOH A 27 427 21 HOH HOH . E 4 HOH A 28 428 28 HOH HOH . E 4 HOH A 29 429 2 HOH HOH . E 4 HOH A 30 430 48 HOH HOH . E 4 HOH A 31 431 132 HOH HOH . E 4 HOH A 32 432 66 HOH HOH . E 4 HOH A 33 433 18 HOH HOH . E 4 HOH A 34 434 53 HOH HOH . E 4 HOH A 35 435 140 HOH HOH . E 4 HOH A 36 436 70 HOH HOH . E 4 HOH A 37 437 65 HOH HOH . E 4 HOH A 38 438 8 HOH HOH . E 4 HOH A 39 439 104 HOH HOH . E 4 HOH A 40 440 128 HOH HOH . E 4 HOH A 41 441 54 HOH HOH . E 4 HOH A 42 442 123 HOH HOH . E 4 HOH A 43 443 23 HOH HOH . E 4 HOH A 44 444 89 HOH HOH . E 4 HOH A 45 445 105 HOH HOH . E 4 HOH A 46 446 86 HOH HOH . E 4 HOH A 47 447 94 HOH HOH . E 4 HOH A 48 448 55 HOH HOH . E 4 HOH A 49 449 24 HOH HOH . E 4 HOH A 50 450 129 HOH HOH . E 4 HOH A 51 451 58 HOH HOH . E 4 HOH A 52 452 137 HOH HOH . E 4 HOH A 53 453 113 HOH HOH . E 4 HOH A 54 454 125 HOH HOH . E 4 HOH A 55 455 127 HOH HOH . E 4 HOH A 56 456 108 HOH HOH . E 4 HOH A 57 457 46 HOH HOH . E 4 HOH A 58 458 50 HOH HOH . E 4 HOH A 59 459 96 HOH HOH . E 4 HOH A 60 460 56 HOH HOH . E 4 HOH A 61 461 97 HOH HOH . E 4 HOH A 62 462 101 HOH HOH . E 4 HOH A 63 463 35 HOH HOH . E 4 HOH A 64 464 43 HOH HOH . E 4 HOH A 65 465 31 HOH HOH . E 4 HOH A 66 466 82 HOH HOH . E 4 HOH A 67 467 135 HOH HOH . E 4 HOH A 68 468 76 HOH HOH . E 4 HOH A 69 469 121 HOH HOH . E 4 HOH A 70 470 131 HOH HOH . E 4 HOH A 71 471 138 HOH HOH . E 4 HOH A 72 472 87 HOH HOH . E 4 HOH A 73 473 78 HOH HOH . E 4 HOH A 74 474 114 HOH HOH . E 4 HOH A 75 475 136 HOH HOH . E 4 HOH A 76 476 99 HOH HOH . E 4 HOH A 77 477 130 HOH HOH . E 4 HOH A 78 478 80 HOH HOH . F 4 HOH B 1 501 152 HOH HOH . F 4 HOH B 2 502 141 HOH HOH . F 4 HOH B 3 503 19 HOH HOH . F 4 HOH B 4 504 144 HOH HOH . F 4 HOH B 5 505 15 HOH HOH . F 4 HOH B 6 506 85 HOH HOH . F 4 HOH B 7 507 106 HOH HOH . F 4 HOH B 8 508 69 HOH HOH . F 4 HOH B 9 509 61 HOH HOH . F 4 HOH B 10 510 42 HOH HOH . F 4 HOH B 11 511 117 HOH HOH . F 4 HOH B 12 512 83 HOH HOH . F 4 HOH B 13 513 3 HOH HOH . F 4 HOH B 14 514 9 HOH HOH . F 4 HOH B 15 515 41 HOH HOH . F 4 HOH B 16 516 13 HOH HOH . F 4 HOH B 17 517 1 HOH HOH . F 4 HOH B 18 518 44 HOH HOH . F 4 HOH B 19 519 150 HOH HOH . F 4 HOH B 20 520 27 HOH HOH . F 4 HOH B 21 521 90 HOH HOH . F 4 HOH B 22 522 29 HOH HOH . F 4 HOH B 23 523 98 HOH HOH . F 4 HOH B 24 524 17 HOH HOH . F 4 HOH B 25 525 49 HOH HOH . F 4 HOH B 26 526 147 HOH HOH . F 4 HOH B 27 527 109 HOH HOH . F 4 HOH B 28 528 124 HOH HOH . F 4 HOH B 29 529 38 HOH HOH . F 4 HOH B 30 530 64 HOH HOH . F 4 HOH B 31 531 75 HOH HOH . F 4 HOH B 32 532 4 HOH HOH . F 4 HOH B 33 533 39 HOH HOH . F 4 HOH B 34 534 60 HOH HOH . F 4 HOH B 35 535 5 HOH HOH . F 4 HOH B 36 536 73 HOH HOH . F 4 HOH B 37 537 84 HOH HOH . F 4 HOH B 38 538 148 HOH HOH . F 4 HOH B 39 539 63 HOH HOH . F 4 HOH B 40 540 47 HOH HOH . F 4 HOH B 41 541 57 HOH HOH . F 4 HOH B 42 542 25 HOH HOH . F 4 HOH B 43 543 74 HOH HOH . F 4 HOH B 44 544 93 HOH HOH . F 4 HOH B 45 545 120 HOH HOH . F 4 HOH B 46 546 32 HOH HOH . F 4 HOH B 47 547 122 HOH HOH . F 4 HOH B 48 548 12 HOH HOH . F 4 HOH B 49 549 52 HOH HOH . F 4 HOH B 50 550 149 HOH HOH . F 4 HOH B 51 551 7 HOH HOH . F 4 HOH B 52 552 71 HOH HOH . F 4 HOH B 53 553 126 HOH HOH . F 4 HOH B 54 554 151 HOH HOH . F 4 HOH B 55 555 110 HOH HOH . F 4 HOH B 56 556 153 HOH HOH . F 4 HOH B 57 557 118 HOH HOH . F 4 HOH B 58 558 143 HOH HOH . F 4 HOH B 59 559 119 HOH HOH . F 4 HOH B 60 560 145 HOH HOH . F 4 HOH B 61 561 81 HOH HOH . F 4 HOH B 62 562 142 HOH HOH . F 4 HOH B 63 563 68 HOH HOH . F 4 HOH B 64 564 111 HOH HOH . F 4 HOH B 65 565 146 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 6.423 -29.962 -43.709 1 95.42 ? C1 MPD 402 B 1 HETATM 2 C C2 MPD . . . D 3 7.715 -30.656 -43.319 1 86.1 ? C2 MPD 402 B 1 HETATM 3 O O2 MPD . . . D 3 8.068 -30.442 -41.926 1 79.97 ? O2 MPD 402 B 1 HETATM 4 C CM MPD . . . D 3 7.484 -32.151 -43.518 1 78.24 ? CM MPD 402 B 1 HETATM 5 C C3 MPD . . . D 3 8.804 -30.046 -44.202 1 83.41 ? C3 MPD 402 B 1 HETATM 6 C C4 MPD . . . D 3 8.381 -28.666 -44.717 1 84.72 ? C4 MPD 402 B 1 HETATM 7 O O4 MPD . . . D 3 8.946 -27.657 -43.921 1 87.43 ? O4 MPD 402 B 1 HETATM 8 C C5 MPD . . . D 3 8.774 -28.438 -46.165 1 92.03 ? C5 MPD 402 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 8 #