data_8XND # _model_server_result.job_id Ulgj7gFJgndYla5q61viEA _model_server_result.datetime_utc '2025-07-13 06:28:51' _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":"E","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 . . . E 2 -19.008 75.389 52.515 1 78.99 ? N1 PLP 500 A 1 HETATM 2 C C2 PLP . . . E 2 -18.796 76.058 53.629 1 84.29 ? C2 PLP 500 A 1 HETATM 3 C C2A PLP . . . E 2 -19.289 75.426 54.882 1 86.56 ? C2A PLP 500 A 1 HETATM 4 C C3 PLP . . . E 2 -18.124 77.303 53.608 1 96.98 ? C3 PLP 500 A 1 HETATM 5 O O3 PLP . . . E 2 -17.855 78.076 54.713 1 120.4 ? O3 PLP 500 A 1 HETATM 6 C C4 PLP . . . E 2 -17.677 77.848 52.389 1 109.05 ? C4 PLP 500 A 1 HETATM 7 C C4A PLP . . . E 2 -16.943 79.12 52.406 1 118.03 ? C4A PLP 500 A 1 HETATM 8 C C5 PLP . . . E 2 -17.946 77.123 51.212 1 109.62 ? C5 PLP 500 A 1 HETATM 9 C C6 PLP . . . E 2 -18.57 75.908 51.345 1 118.55 ? C6 PLP 500 A 1 HETATM 10 C C5A PLP . . . E 2 -17.477 77.541 49.842 1 78.71 ? C5A PLP 500 A 1 HETATM 11 O O4P PLP . . . E 2 -17.826 78.87 49.36 1 69.17 ? O4P PLP 500 A 1 HETATM 12 P P PLP . . . E 2 -16.964 79.332 48.036 1 83.12 ? P PLP 500 A 1 HETATM 13 O O1P PLP . . . E 2 -17.533 78.55 46.811 1 80.16 ? O1P PLP 500 A 1 HETATM 14 O O2P PLP . . . E 2 -15.502 78.963 48.343 1 82.63 ? O2P PLP 500 A 1 HETATM 15 O O3P PLP . . . E 2 -17.113 80.855 47.855 1 81.55 ? O3P PLP 500 A 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 15 #