data_2D7Y # _model_server_result.job_id EUecbbruwqlbxZ6Wa1mI9g _model_server_result.datetime_utc '2025-03-06 10:30:19' _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 2d7y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":413}' # _entry.id 2D7Y # _exptl.entry_id 2D7Y _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 90 _cell.angle_gamma 90 _cell.entry_id 2D7Y _cell.length_a 155.948 _cell.length_b 87.793 _cell.length_c 80.065 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2D7Y _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,PQS _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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 246 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 258 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C4A _struct_conn.ptnr2_label_comp_id PLP _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id PLP _struct_conn.ptnr2_auth_seq_id 413 _struct_conn.ptnr2_symmetry 1_555 _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 1.378 _struct_conn.pdbx_value_order ? # _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' # _atom_sites.entry_id 2D7Y _atom_sites.fract_transf_matrix[1][1] 0.006412 _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] 0.01139 _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] 0.01249 _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 1 413 413 PLP PLP . C 3 HOH A 1 414 1 HOH HOH . C 3 HOH A 2 415 2 HOH HOH . C 3 HOH A 3 416 3 HOH HOH . C 3 HOH A 4 417 4 HOH HOH . C 3 HOH A 5 418 5 HOH HOH . C 3 HOH A 6 419 6 HOH HOH . C 3 HOH A 7 420 7 HOH HOH . C 3 HOH A 8 421 8 HOH HOH . C 3 HOH A 9 422 9 HOH HOH . C 3 HOH A 10 423 11 HOH HOH . C 3 HOH A 11 424 12 HOH HOH . C 3 HOH A 12 425 13 HOH HOH . C 3 HOH A 13 426 14 HOH HOH . C 3 HOH A 14 427 15 HOH HOH . C 3 HOH A 15 428 16 HOH HOH . C 3 HOH A 16 429 17 HOH HOH . C 3 HOH A 17 430 21 HOH HOH . C 3 HOH A 18 431 22 HOH HOH . C 3 HOH A 19 432 23 HOH HOH . C 3 HOH A 20 433 24 HOH HOH . C 3 HOH A 21 434 25 HOH HOH . C 3 HOH A 22 435 27 HOH HOH . C 3 HOH A 23 436 29 HOH HOH . C 3 HOH A 24 437 30 HOH HOH . C 3 HOH A 25 438 33 HOH HOH . C 3 HOH A 26 439 34 HOH HOH . C 3 HOH A 27 440 37 HOH HOH . C 3 HOH A 28 441 38 HOH HOH . C 3 HOH A 29 442 41 HOH HOH . C 3 HOH A 30 443 43 HOH HOH . C 3 HOH A 31 444 44 HOH HOH . C 3 HOH A 32 445 45 HOH HOH . C 3 HOH A 33 446 46 HOH HOH . C 3 HOH A 34 447 48 HOH HOH . C 3 HOH A 35 448 49 HOH HOH . C 3 HOH A 36 449 50 HOH HOH . C 3 HOH A 37 450 54 HOH HOH . C 3 HOH A 38 451 56 HOH HOH . C 3 HOH A 39 452 58 HOH HOH . C 3 HOH A 40 453 59 HOH HOH . C 3 HOH A 41 454 60 HOH HOH . C 3 HOH A 42 455 61 HOH HOH . C 3 HOH A 43 456 63 HOH HOH . C 3 HOH A 44 457 64 HOH HOH . C 3 HOH A 45 458 65 HOH HOH . C 3 HOH A 46 459 66 HOH HOH . C 3 HOH A 47 460 68 HOH HOH . C 3 HOH A 48 461 69 HOH HOH . C 3 HOH A 49 462 70 HOH HOH . C 3 HOH A 50 463 72 HOH HOH . C 3 HOH A 51 464 73 HOH HOH . C 3 HOH A 52 465 74 HOH HOH . C 3 HOH A 53 466 75 HOH HOH . C 3 HOH A 54 467 76 HOH HOH . C 3 HOH A 55 468 77 HOH HOH . C 3 HOH A 56 469 78 HOH HOH . C 3 HOH A 57 470 79 HOH HOH . C 3 HOH A 58 471 80 HOH HOH . C 3 HOH A 59 472 81 HOH HOH . C 3 HOH A 60 473 82 HOH HOH . C 3 HOH A 61 474 83 HOH HOH . C 3 HOH A 62 475 84 HOH HOH . C 3 HOH A 63 476 86 HOH HOH . C 3 HOH A 64 477 87 HOH HOH . C 3 HOH A 65 478 91 HOH HOH . C 3 HOH A 66 479 95 HOH HOH . C 3 HOH A 67 480 96 HOH HOH . C 3 HOH A 68 481 97 HOH HOH . C 3 HOH A 69 482 99 HOH HOH . C 3 HOH A 70 483 105 HOH HOH . C 3 HOH A 71 484 108 HOH HOH . C 3 HOH A 72 485 109 HOH HOH . C 3 HOH A 73 486 110 HOH HOH . C 3 HOH A 74 487 113 HOH HOH . C 3 HOH A 75 488 124 HOH HOH . C 3 HOH A 76 489 127 HOH HOH . C 3 HOH A 77 490 128 HOH HOH . C 3 HOH A 78 491 134 HOH HOH . C 3 HOH A 79 492 135 HOH HOH . C 3 HOH A 80 493 137 HOH HOH . C 3 HOH A 81 494 138 HOH HOH . C 3 HOH A 82 495 149 HOH HOH . C 3 HOH A 83 496 153 HOH HOH . C 3 HOH A 84 497 154 HOH HOH . C 3 HOH A 85 498 156 HOH HOH . C 3 HOH A 86 499 163 HOH HOH . C 3 HOH A 87 500 181 HOH HOH . C 3 HOH A 88 501 186 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 26.822 5.215 -14.727 1 17.06 ? N1 PLP 413 A 1 HETATM 2 C C2 PLP . . . B 2 26.432 6.365 -15.391 1 17.73 ? C2 PLP 413 A 1 HETATM 3 C C2A PLP . . . B 2 27.39 6.845 -16.484 1 17.97 ? C2A PLP 413 A 1 HETATM 4 C C3 PLP . . . B 2 25.229 6.968 -15.02 1 18.15 ? C3 PLP 413 A 1 HETATM 5 O O3 PLP . . . B 2 24.891 8.098 -15.703 1 18.37 ? O3 PLP 413 A 1 HETATM 6 C C4 PLP . . . B 2 24.4 6.461 -14.014 1 20.57 ? C4 PLP 413 A 1 HETATM 7 C C4A PLP . . . B 2 23.059 7.166 -13.649 1 20.68 ? C4A PLP 413 A 1 HETATM 8 C C5 PLP . . . B 2 24.811 5.263 -13.328 1 18.45 ? C5 PLP 413 A 1 HETATM 9 C C6 PLP . . . B 2 26.017 4.705 -13.731 1 16.73 ? C6 PLP 413 A 1 HETATM 10 C C5A PLP . . . B 2 24.07 4.547 -12.219 1 17.67 ? C5A PLP 413 A 1 HETATM 11 O O4P PLP . . . B 2 23.654 5.345 -11.143 1 19.58 ? O4P PLP 413 A 1 HETATM 12 P P PLP . . . B 2 22.522 4.911 -10.18 1 19.69 ? P PLP 413 A 1 HETATM 13 O O1P PLP . . . B 2 22.142 5.838 -9.087 1 18.33 ? O1P PLP 413 A 1 HETATM 14 O O2P PLP . . . B 2 22.163 3.45 -10.168 1 18.28 ? O2P PLP 413 A 1 HETATM 15 O O3P PLP . . . B 2 23.627 4.526 -9.263 1 15.69 ? O3P PLP 413 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 239 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 15 #