data_8XND # _model_server_result.job_id multGtDHhDbiFbY7q3bGMQ _model_server_result.datetime_utc '2025-07-10 19:53:21' _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 8xnd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":500}' # _entry.id 8XND # _exptl.entry_id 8XND _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 4 _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 120 _cell.entry_id 8XND _cell.length_a 151.54 _cell.length_b 151.54 _cell.length_c 234.97 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XND _symmetry.cell_setting ? _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,H 1 1 B,C,F,G 2 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N 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 258 n y N1 C6 PLP sing 259 n y C2 C2A PLP sing 260 n n C2 C3 PLP sing 261 n y C2A H2A1 PLP sing 262 n n C2A H2A2 PLP sing 263 n n C2A H2A3 PLP sing 264 n n C3 O3 PLP sing 265 n n C3 C4 PLP doub 266 n y O3 HO3 PLP sing 267 n n C4 C4A PLP sing 268 n n C4 C5 PLP sing 269 n y C4A O4A PLP doub 270 n n C4A H4A PLP sing 271 n n C5 C6 PLP doub 272 n y C5 C5A PLP sing 273 n n C6 H6 PLP sing 274 n n C5A O4P PLP sing 275 n n C5A H5A1 PLP sing 276 n n C5A H5A2 PLP sing 277 n n O4P P PLP sing 278 n n P O1P PLP doub 279 n n P O2P PLP sing 280 n n P O3P PLP sing 281 n n O2P HOP2 PLP sing 282 n n O3P HOP3 PLP sing 283 n n # _atom_sites.entry_id 8XND _atom_sites.fract_transf_matrix[1][1] 0.006599 _atom_sites.fract_transf_matrix[1][2] 0.00381 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00762 _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] 0.004256 _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 E 2 PLP A 1 500 500 PLP PLP . F 2 PLP B 1 500 500 PLP PLP . G 2 PLP C 1 500 500 PLP PLP . H 2 PLP D 1 500 500 PLP PLP . # 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 . . . G 2 -57.036 55.755 52.428 1 60.99 ? N1 PLP 500 C 1 HETATM 2 C C2 PLP . . . G 2 -57.625 55.146 53.432 1 54.6 ? C2 PLP 500 C 1 HETATM 3 C C2A PLP . . . G 2 -57.301 55.678 54.784 1 63.23 ? C2A PLP 500 C 1 HETATM 4 C C3 PLP . . . G 2 -58.561 54.11 53.192 1 56.74 ? C3 PLP 500 C 1 HETATM 5 O O3 PLP . . . G 2 -59.292 53.455 54.125 1 64.92 ? O3 PLP 500 C 1 HETATM 6 C C4 PLP . . . G 2 -58.782 53.647 51.873 1 80.26 ? C4 PLP 500 C 1 HETATM 7 C C4A PLP . . . G 2 -59.76 52.587 51.593 1 65.28 ? C4A PLP 500 C 1 HETATM 8 C C5 PLP . . . G 2 -58.073 54.266 50.827 1 97.17 ? C5 PLP 500 C 1 HETATM 9 C C6 PLP . . . G 2 -57.244 55.311 51.162 1 95.99 ? C6 PLP 500 C 1 HETATM 10 C C5A PLP . . . G 2 -58.279 53.89 49.386 1 76.13 ? C5A PLP 500 C 1 HETATM 11 O O4P PLP . . . G 2 -57.916 52.531 49.004 1 70.34 ? O4P PLP 500 C 1 HETATM 12 P P PLP . . . G 2 -58.706 51.919 47.703 1 84.1 ? P PLP 500 C 1 HETATM 13 O O1P PLP . . . G 2 -58.078 52.639 46.44 1 49.51 ? O1P PLP 500 C 1 HETATM 14 O O2P PLP . . . G 2 -60.174 52.249 47.972 1 87.95 ? O2P PLP 500 C 1 HETATM 15 O O3P PLP . . . G 2 -58.579 50.378 47.694 1 85.33 ? O3P PLP 500 C 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 15 #