data_5OFY # _model_server_result.job_id MtXJN_UcHQZZfqMrikErUg _model_server_result.datetime_utc '2024-11-26 01:39:29' _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 5ofy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5OFY # _exptl.entry_id 5OFY _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 5OFY _cell.length_a 89.049 _cell.length_b 89.049 _cell.length_c 140.864 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OFY _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _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,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' 7_555 y,x,-z 0 1 0 1 0 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 209 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 209 _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 401 _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 1.448 _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' # 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 274 n y N1 C6 PLP sing 275 n y C2 C2A PLP sing 276 n n C2 C3 PLP sing 277 n y C2A H2A1 PLP sing 278 n n C2A H2A2 PLP sing 279 n n C2A H2A3 PLP sing 280 n n C3 O3 PLP sing 281 n n C3 C4 PLP doub 282 n y O3 HO3 PLP sing 283 n n C4 C4A PLP sing 284 n n C4 C5 PLP sing 285 n y C4A O4A PLP doub 286 n n C4A H4A PLP sing 287 n n C5 C6 PLP doub 288 n y C5 C5A PLP sing 289 n n C6 H6 PLP sing 290 n n C5A O4P PLP sing 291 n n C5A H5A1 PLP sing 292 n n C5A H5A2 PLP sing 293 n n O4P P PLP sing 294 n n P O1P PLP doub 295 n n P O2P PLP sing 296 n n P O3P PLP sing 297 n n O2P HOP2 PLP sing 298 n n O3P HOP3 PLP sing 299 n n # _atom_sites.entry_id 5OFY _atom_sites.fract_transf_matrix[1][1] 0.01123 _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] 0.01123 _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] 0.007099 _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 1 401 1209 PLP PLP . C 3 DIO A 1 402 1 DIO DIO . D 4 HOH A 1 501 11 HOH HOH . D 4 HOH A 2 502 22 HOH HOH . D 4 HOH A 3 503 13 HOH HOH . D 4 HOH A 4 504 27 HOH HOH . D 4 HOH A 5 505 24 HOH HOH . D 4 HOH A 6 506 7 HOH HOH . D 4 HOH A 7 507 9 HOH HOH . D 4 HOH A 8 508 20 HOH HOH . D 4 HOH A 9 509 33 HOH HOH . D 4 HOH A 10 510 3 HOH HOH . D 4 HOH A 11 511 19 HOH HOH . D 4 HOH A 12 512 6 HOH HOH . D 4 HOH A 13 513 30 HOH HOH . D 4 HOH A 14 514 4 HOH HOH . D 4 HOH A 15 515 12 HOH HOH . D 4 HOH A 16 516 29 HOH HOH . D 4 HOH A 17 517 21 HOH HOH . D 4 HOH A 18 518 26 HOH HOH . D 4 HOH A 19 519 14 HOH HOH . D 4 HOH A 20 520 23 HOH HOH . D 4 HOH A 21 521 18 HOH HOH . D 4 HOH A 22 522 31 HOH HOH . D 4 HOH A 23 523 2 HOH HOH . D 4 HOH A 24 524 28 HOH HOH . D 4 HOH A 25 525 32 HOH HOH . D 4 HOH A 26 526 5 HOH HOH . D 4 HOH A 27 527 25 HOH HOH . D 4 HOH A 28 528 10 HOH HOH . D 4 HOH A 29 529 16 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 -12.679 -8.159 -15.111 1 97.14 ? N1 PLP 401 A 1 HETATM 2 C C2 PLP . . . B 2 -13.323 -8.885 -16.054 1 101.21 ? C2 PLP 401 A 1 HETATM 3 C C2A PLP . . . B 2 -12.731 -9.07 -17.423 1 102.25 ? C2A PLP 401 A 1 HETATM 4 C C3 PLP . . . B 2 -14.626 -9.508 -15.74 1 98.45 ? C3 PLP 401 A 1 HETATM 5 O O3 PLP . . . B 2 -15.266 -10.235 -16.683 1 107.4 ? O3 PLP 401 A 1 HETATM 6 C C4 PLP . . . B 2 -15.196 -9.315 -14.386 1 92.12 ? C4 PLP 401 A 1 HETATM 7 C C4A PLP . . . B 2 -16.524 -9.888 -13.941 1 83.31 ? C4A PLP 401 A 1 HETATM 8 C C5 PLP . . . B 2 -14.389 -8.513 -13.426 1 91.84 ? C5 PLP 401 A 1 HETATM 9 C C6 PLP . . . B 2 -13.172 -7.969 -13.87 1 97.94 ? C6 PLP 401 A 1 HETATM 10 C C5A PLP . . . B 2 -14.908 -8.218 -12.017 1 82.24 ? C5A PLP 401 A 1 HETATM 11 O O4P PLP . . . B 2 -14.469 -9.068 -10.961 1 71.01 ? O4P PLP 401 A 1 HETATM 12 P P PLP . . . B 2 -15.036 -8.74 -9.488 1 66.82 ? P PLP 401 A 1 HETATM 13 O O1P PLP . . . B 2 -16.072 -7.697 -9.78 1 54.65 ? O1P PLP 401 A 1 HETATM 14 O O2P PLP . . . B 2 -13.879 -8.299 -8.614 1 67.4 ? O2P PLP 401 A 1 HETATM 15 O O3P PLP . . . B 2 -15.55 -10.071 -9.035 1 75.29 ? O3P PLP 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #