data_2D7Z # _model_server_result.job_id 8_uPm4uFmLtcXmWKn0gvCQ _model_server_result.datetime_utc '2025-03-06 10:18:03' _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 2d7z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":413}' # _entry.id 2D7Z # _exptl.entry_id 2D7Z _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 2D7Z _cell.length_a 157.354 _cell.length_b 85.415 _cell.length_c 78.621 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2D7Z _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,D _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 1.39 _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 2D7Z _atom_sites.fract_transf_matrix[1][1] 0.006355 _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] 0.011708 _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] 0.012719 _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 MAE A 1 414 414 MAE MAE . D 4 HOH A 1 415 1 HOH HOH . D 4 HOH A 2 416 2 HOH HOH . D 4 HOH A 3 417 3 HOH HOH . D 4 HOH A 4 418 4 HOH HOH . D 4 HOH A 5 419 5 HOH HOH . D 4 HOH A 6 420 6 HOH HOH . D 4 HOH A 7 421 8 HOH HOH . D 4 HOH A 8 422 9 HOH HOH . D 4 HOH A 9 423 10 HOH HOH . D 4 HOH A 10 424 11 HOH HOH . D 4 HOH A 11 425 12 HOH HOH . D 4 HOH A 12 426 14 HOH HOH . D 4 HOH A 13 427 15 HOH HOH . D 4 HOH A 14 428 16 HOH HOH . D 4 HOH A 15 429 17 HOH HOH . D 4 HOH A 16 430 18 HOH HOH . D 4 HOH A 17 431 19 HOH HOH . D 4 HOH A 18 432 20 HOH HOH . D 4 HOH A 19 433 21 HOH HOH . D 4 HOH A 20 434 22 HOH HOH . D 4 HOH A 21 435 24 HOH HOH . D 4 HOH A 22 436 25 HOH HOH . D 4 HOH A 23 437 26 HOH HOH . D 4 HOH A 24 438 28 HOH HOH . D 4 HOH A 25 439 29 HOH HOH . D 4 HOH A 26 440 30 HOH HOH . D 4 HOH A 27 441 31 HOH HOH . D 4 HOH A 28 442 32 HOH HOH . D 4 HOH A 29 443 33 HOH HOH . D 4 HOH A 30 444 34 HOH HOH . D 4 HOH A 31 445 35 HOH HOH . D 4 HOH A 32 446 37 HOH HOH . D 4 HOH A 33 447 38 HOH HOH . D 4 HOH A 34 448 39 HOH HOH . D 4 HOH A 35 449 40 HOH HOH . D 4 HOH A 36 450 41 HOH HOH . D 4 HOH A 37 451 42 HOH HOH . D 4 HOH A 38 452 43 HOH HOH . D 4 HOH A 39 453 46 HOH HOH . D 4 HOH A 40 454 50 HOH HOH . D 4 HOH A 41 455 51 HOH HOH . D 4 HOH A 42 456 52 HOH HOH . D 4 HOH A 43 457 53 HOH HOH . D 4 HOH A 44 458 56 HOH HOH . D 4 HOH A 45 459 58 HOH HOH . D 4 HOH A 46 460 60 HOH HOH . D 4 HOH A 47 461 63 HOH HOH . D 4 HOH A 48 462 65 HOH HOH . D 4 HOH A 49 463 66 HOH HOH . D 4 HOH A 50 464 67 HOH HOH . D 4 HOH A 51 465 69 HOH HOH . D 4 HOH A 52 466 70 HOH HOH . D 4 HOH A 53 467 73 HOH HOH . D 4 HOH A 54 468 75 HOH HOH . D 4 HOH A 55 469 77 HOH HOH . D 4 HOH A 56 470 78 HOH HOH . D 4 HOH A 57 471 79 HOH HOH . D 4 HOH A 58 472 81 HOH HOH . D 4 HOH A 59 473 82 HOH HOH . D 4 HOH A 60 474 83 HOH HOH . D 4 HOH A 61 475 85 HOH HOH . D 4 HOH A 62 476 87 HOH HOH . D 4 HOH A 63 477 89 HOH HOH . D 4 HOH A 64 478 92 HOH HOH . D 4 HOH A 65 479 93 HOH HOH . D 4 HOH A 66 480 94 HOH HOH . D 4 HOH A 67 481 97 HOH HOH . D 4 HOH A 68 482 98 HOH HOH . D 4 HOH A 69 483 99 HOH HOH . D 4 HOH A 70 484 100 HOH HOH . D 4 HOH A 71 485 101 HOH HOH . D 4 HOH A 72 486 103 HOH HOH . D 4 HOH A 73 487 111 HOH HOH . D 4 HOH A 74 488 112 HOH HOH . D 4 HOH A 75 489 122 HOH HOH . D 4 HOH A 76 490 123 HOH HOH . D 4 HOH A 77 491 138 HOH HOH . D 4 HOH A 78 492 143 HOH HOH . D 4 HOH A 79 493 152 HOH HOH . D 4 HOH A 80 494 154 HOH HOH . D 4 HOH A 81 495 160 HOH HOH . D 4 HOH A 82 496 164 HOH HOH . D 4 HOH A 83 497 178 HOH HOH . D 4 HOH A 84 498 179 HOH HOH . D 4 HOH A 85 499 189 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 26.899 4.678 -15.037 1 26.01 ? N1 PLP 413 A 1 HETATM 2 C C2 PLP . . . B 2 26.395 5.717 -15.791 1 27.27 ? C2 PLP 413 A 1 HETATM 3 C C2A PLP . . . B 2 27.216 6.093 -17.016 1 28.26 ? C2A PLP 413 A 1 HETATM 4 C C3 PLP . . . B 2 25.207 6.318 -15.381 1 29.64 ? C3 PLP 413 A 1 HETATM 5 O O3 PLP . . . B 2 24.756 7.349 -16.174 1 28.48 ? O3 PLP 413 A 1 HETATM 6 C C4 PLP . . . B 2 24.496 5.915 -14.237 1 29.66 ? C4 PLP 413 A 1 HETATM 7 C C4A PLP . . . B 2 23.161 6.63 -13.845 1 33.08 ? C4A PLP 413 A 1 HETATM 8 C C5 PLP . . . B 2 25.029 4.826 -13.453 1 27.63 ? C5 PLP 413 A 1 HETATM 9 C C6 PLP . . . B 2 26.217 4.27 -13.912 1 25.15 ? C6 PLP 413 A 1 HETATM 10 C C5A PLP . . . B 2 24.458 4.193 -12.183 1 27.01 ? C5A PLP 413 A 1 HETATM 11 O O4P PLP . . . B 2 23.55 4.926 -11.397 1 24.03 ? O4P PLP 413 A 1 HETATM 12 P P PLP . . . B 2 22.937 4.32 -10.11 1 22.06 ? P PLP 413 A 1 HETATM 13 O O1P PLP . . . B 2 22.068 5.421 -9.632 1 24.05 ? O1P PLP 413 A 1 HETATM 14 O O2P PLP . . . B 2 24.059 4.06 -9.163 1 22.17 ? O2P PLP 413 A 1 HETATM 15 O O3P PLP . . . B 2 22.183 3.117 -10.439 1 22.57 ? O3P PLP 413 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 15 #