data_8YRT # _model_server_result.job_id ExPubqJD5sUBsKN5NPR2yw _model_server_result.datetime_utc '2024-11-14 16:47:37' _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 8yrt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 8YRT # _exptl.entry_id 8YRT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _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 100.14 _cell.angle_gamma 90 _cell.entry_id 8YRT _cell.length_a 86.043 _cell.length_b 71.902 _cell.length_c 52.015 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YRT _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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 _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' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 76.885551 0 51.202552 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C8 H10 N O6 P' _chem_comp.formula_weight 247.142 _chem_comp.id PLP _chem_comp.mon_nstd_flag . _chem_comp.name "PYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN B6 Phosphate' # 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 N1 C2 PLP doub 260 n y N1 C6 PLP sing 261 n y C2 C2A PLP sing 262 n n C2 C3 PLP sing 263 n y C2A H2A1 PLP sing 264 n n C2A H2A2 PLP sing 265 n n C2A H2A3 PLP sing 266 n n C3 O3 PLP sing 267 n n C3 C4 PLP doub 268 n y O3 HO3 PLP sing 269 n n C4 C4A PLP sing 270 n n C4 C5 PLP sing 271 n y C4A O4A PLP doub 272 n n C4A H4A PLP sing 273 n n C5 C6 PLP doub 274 n y C5 C5A PLP sing 275 n n C6 H6 PLP sing 276 n n C5A O4P PLP sing 277 n n C5A H5A1 PLP sing 278 n n C5A H5A2 PLP sing 279 n n O4P P PLP sing 280 n n P O1P PLP doub 281 n n P O2P PLP sing 282 n n P O3P PLP sing 283 n n O2P HOP2 PLP sing 284 n n O3P HOP3 PLP sing 285 n n # _atom_sites.entry_id 8YRT _atom_sites.fract_transf_matrix[1][1] 0.011622 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002079 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013908 _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] 0.01953 _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 PLP A 1 301 301 PLP 00F . C 3 HOH A 1 401 95 HOH HOH . C 3 HOH A 2 402 68 HOH HOH . C 3 HOH A 3 403 53 HOH HOH . C 3 HOH A 4 404 32 HOH HOH . C 3 HOH A 5 405 106 HOH HOH . C 3 HOH A 6 406 97 HOH HOH . C 3 HOH A 7 407 10 HOH HOH . C 3 HOH A 8 408 100 HOH HOH . C 3 HOH A 9 409 9 HOH HOH . C 3 HOH A 10 410 109 HOH HOH . C 3 HOH A 11 411 12 HOH HOH . C 3 HOH A 12 412 62 HOH HOH . C 3 HOH A 13 413 2 HOH HOH . C 3 HOH A 14 414 91 HOH HOH . C 3 HOH A 15 415 93 HOH HOH . C 3 HOH A 16 416 38 HOH HOH . C 3 HOH A 17 417 120 HOH HOH . C 3 HOH A 18 418 6 HOH HOH . C 3 HOH A 19 419 78 HOH HOH . C 3 HOH A 20 420 115 HOH HOH . C 3 HOH A 21 421 8 HOH HOH . C 3 HOH A 22 422 20 HOH HOH . C 3 HOH A 23 423 41 HOH HOH . C 3 HOH A 24 424 47 HOH HOH . C 3 HOH A 25 425 112 HOH HOH . C 3 HOH A 26 426 30 HOH HOH . C 3 HOH A 27 427 21 HOH HOH . C 3 HOH A 28 428 64 HOH HOH . C 3 HOH A 29 429 122 HOH HOH . C 3 HOH A 30 430 113 HOH HOH . C 3 HOH A 31 431 127 HOH HOH . C 3 HOH A 32 432 25 HOH HOH . C 3 HOH A 33 433 70 HOH HOH . C 3 HOH A 34 434 3 HOH HOH . C 3 HOH A 35 435 31 HOH HOH . C 3 HOH A 36 436 26 HOH HOH . C 3 HOH A 37 437 76 HOH HOH . C 3 HOH A 38 438 123 HOH HOH . C 3 HOH A 39 439 44 HOH HOH . C 3 HOH A 40 440 58 HOH HOH . C 3 HOH A 41 441 108 HOH HOH . C 3 HOH A 42 442 13 HOH HOH . C 3 HOH A 43 443 39 HOH HOH . C 3 HOH A 44 444 66 HOH HOH . C 3 HOH A 45 445 67 HOH HOH . C 3 HOH A 46 446 27 HOH HOH . C 3 HOH A 47 447 61 HOH HOH . C 3 HOH A 48 448 111 HOH HOH . C 3 HOH A 49 449 45 HOH HOH . C 3 HOH A 50 450 24 HOH HOH . C 3 HOH A 51 451 75 HOH HOH . C 3 HOH A 52 452 48 HOH HOH . C 3 HOH A 53 453 98 HOH HOH . C 3 HOH A 54 454 73 HOH HOH . C 3 HOH A 55 455 19 HOH HOH . C 3 HOH A 56 456 37 HOH HOH . C 3 HOH A 57 457 7 HOH HOH . C 3 HOH A 58 458 5 HOH HOH . C 3 HOH A 59 459 1 HOH HOH . C 3 HOH A 60 460 128 HOH HOH . C 3 HOH A 61 461 92 HOH HOH . C 3 HOH A 62 462 72 HOH HOH . C 3 HOH A 63 463 17 HOH HOH . C 3 HOH A 64 464 56 HOH HOH . C 3 HOH A 65 465 22 HOH HOH . C 3 HOH A 66 466 74 HOH HOH . C 3 HOH A 67 467 84 HOH HOH . C 3 HOH A 68 468 60 HOH HOH . C 3 HOH A 69 469 119 HOH HOH . C 3 HOH A 70 470 71 HOH HOH . C 3 HOH A 71 471 116 HOH HOH . C 3 HOH A 72 472 117 HOH HOH . C 3 HOH A 73 473 77 HOH HOH . C 3 HOH A 74 474 114 HOH HOH . C 3 HOH A 75 475 65 HOH HOH . C 3 HOH A 76 476 107 HOH HOH . C 3 HOH A 77 477 130 HOH HOH . C 3 HOH A 78 478 16 HOH HOH . C 3 HOH A 79 479 11 HOH HOH . C 3 HOH A 80 480 89 HOH HOH . C 3 HOH A 81 481 86 HOH HOH . C 3 HOH A 82 482 85 HOH HOH . C 3 HOH A 83 483 94 HOH HOH . C 3 HOH A 84 484 133 HOH HOH . C 3 HOH A 85 485 33 HOH HOH . C 3 HOH A 86 486 55 HOH HOH . C 3 HOH A 87 487 29 HOH HOH . C 3 HOH A 88 488 59 HOH HOH . C 3 HOH A 89 489 50 HOH HOH . C 3 HOH A 90 490 46 HOH HOH . C 3 HOH A 91 491 101 HOH HOH . C 3 HOH A 92 492 14 HOH HOH . C 3 HOH A 93 493 35 HOH HOH . C 3 HOH A 94 494 18 HOH HOH . C 3 HOH A 95 495 121 HOH HOH . C 3 HOH A 96 496 132 HOH HOH . C 3 HOH A 97 497 87 HOH HOH . C 3 HOH A 98 498 23 HOH HOH . C 3 HOH A 99 499 110 HOH HOH . C 3 HOH A 100 500 34 HOH HOH . C 3 HOH A 101 501 40 HOH HOH . C 3 HOH A 102 502 96 HOH HOH . C 3 HOH A 103 503 43 HOH HOH . C 3 HOH A 104 504 90 HOH HOH . C 3 HOH A 105 505 49 HOH HOH . C 3 HOH A 106 506 36 HOH HOH . C 3 HOH A 107 507 82 HOH HOH . C 3 HOH A 108 508 105 HOH HOH . C 3 HOH A 109 509 118 HOH HOH . C 3 HOH A 110 510 99 HOH HOH . C 3 HOH A 111 511 57 HOH HOH . C 3 HOH A 112 512 103 HOH HOH . C 3 HOH A 113 513 131 HOH HOH . C 3 HOH A 114 514 104 HOH HOH . C 3 HOH A 115 515 88 HOH HOH . C 3 HOH A 116 516 102 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 N N1 PLP . . . B 2 27.503 4.229 16.696 1 20.19 ? N1 PLP 301 A 1 HETATM 2 C C2 PLP . . . B 2 28.307 3.388 17.342 1 24.04 ? C2 PLP 301 A 1 HETATM 3 C C2A PLP . . . B 2 29.3 3.92 18.34 1 18.05 ? C2A PLP 301 A 1 HETATM 4 C C3 PLP . . . B 2 28.272 2.007 17.03 1 29.45 ? C3 PLP 301 A 1 HETATM 5 O O3 PLP . . . B 2 29.215 1.195 17.602 1 32 ? O3 PLP 301 A 1 HETATM 6 C C4 PLP . . . B 2 27.356 1.526 16.065 1 26.63 ? C4 PLP 301 A 1 HETATM 7 C C4A PLP . . . B 2 27.439 0.098 15.691 1 36.89 ? C4A PLP 301 A 1 HETATM 8 C C5 PLP . . . B 2 26.434 2.441 15.509 1 22.03 ? C5 PLP 301 A 1 HETATM 9 C C6 PLP . . . B 2 26.551 3.765 15.849 1 20.17 ? C6 PLP 301 A 1 HETATM 10 C C5A PLP . . . B 2 25.413 2.064 14.476 1 17.95 ? C5A PLP 301 A 1 HETATM 11 O O4P PLP . . . B 2 26.037 1.434 13.314 1 15.58 ? O4P PLP 301 A 1 HETATM 12 P P PLP . . . B 2 25.11 0.587 12.279 1 16.06 ? P PLP 301 A 1 HETATM 13 O O1P PLP . . . B 2 26.154 0.197 11.228 1 14.98 ? O1P PLP 301 A 1 HETATM 14 O O2P PLP . . . B 2 24.608 -0.603 13.154 1 14.85 ? O2P PLP 301 A 1 HETATM 15 O O3P PLP . . . B 2 23.87 1.387 11.858 1 15.31 ? O3P PLP 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 21 _model_server_stats.element_count 15 #