data_7E13 # _model_server_result.job_id FSXVZLa-A8RHRESyU2ypVw _model_server_result.datetime_utc '2024-12-21 15:43:50' _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 7e13 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":601}' # _entry.id 7E13 # _exptl.entry_id 7E13 _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 3 _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 7E13 _cell.length_a 121.868 _cell.length_b 121.868 _cell.length_c 306.401 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7E13 _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 ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _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 7E13 _atom_sites.fract_transf_matrix[1][1] 0.008206 _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] 0.008206 _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] 0.003264 _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 1 601 601 PLP PLP . F 2 PLP B 1 601 601 PLP PLP . G 2 PLP C 1 601 601 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 -3.741 48.391 -45.398 1 52.11 ? N1 PLP 601 A 1 HETATM 2 C C2 PLP . . . E 2 -3.132 47.469 -44.658 1 54.23 ? C2 PLP 601 A 1 HETATM 3 C C2A PLP . . . E 2 -3.448 47.366 -43.2 1 52.8 ? C2A PLP 601 A 1 HETATM 4 C C3 PLP . . . E 2 -2.191 46.626 -45.236 1 57.17 ? C3 PLP 601 A 1 HETATM 5 O O3 PLP . . . E 2 -1.604 45.719 -44.428 1 53.58 ? O3 PLP 601 A 1 HETATM 6 C C4 PLP . . . E 2 -1.898 46.745 -46.613 1 59.78 ? C4 PLP 601 A 1 HETATM 7 C C4A PLP . . . E 2 -0.902 45.894 -47.246 1 67.75 ? C4A PLP 601 A 1 HETATM 8 O O4A PLP . . . E 2 -1.021 44.712 -47.438 1 73.75 ? O4A PLP 601 A 1 HETATM 9 C C5 PLP . . . E 2 -2.565 47.703 -47.379 1 56.97 ? C5 PLP 601 A 1 HETATM 10 C C6 PLP . . . E 2 -3.451 48.508 -46.714 1 59.1 ? C6 PLP 601 A 1 HETATM 11 C C5A PLP . . . E 2 -2.271 47.941 -48.846 1 54.96 ? C5A PLP 601 A 1 HETATM 12 O O4P PLP . . . E 2 -1.991 46.778 -49.695 1 54.45 ? O4P PLP 601 A 1 HETATM 13 P P PLP . . . E 2 -1.372 46.897 -51.211 1 60.22 ? P PLP 601 A 1 HETATM 14 O O1P PLP . . . E 2 -1.992 45.772 -52.019 1 54.36 ? O1P PLP 601 A 1 HETATM 15 O O2P PLP . . . E 2 0.126 46.734 -51.036 1 55.69 ? O2P PLP 601 A 1 HETATM 16 O O3P PLP . . . E 2 -1.74 48.28 -51.764 1 55.48 ? O3P PLP 601 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 16 #