data_5Z0Q # _model_server_result.job_id uuuuWPr-iVY4qFYAi7iw_g _model_server_result.datetime_utc '2024-12-22 03:49:20' _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 5z0q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":401}' # _entry.id 5Z0Q # _exptl.entry_id 5Z0Q _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 12 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 89.39 _cell.angle_beta 84.58 _cell.angle_gamma 86.56 _cell.entry_id 5Z0Q _cell.length_a 58.123 _cell.length_b 133.59 _cell.length_c 165.703 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Z0Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # 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 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 PISA dimeric 2 author_and_software_defined_assembly 5 PISA dimeric 2 author_and_software_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,M,Q 1 1 B,I,N,U 2 1 C,K,O,W 3 1 D,G,P,S 4 1 F,J,R,V 5 1 H,L,T,X 6 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 M N N ? 2 N N N ? 2 O N N ? 2 P N N ? 2 Q N N ? 2 R N N ? 2 S N N ? 2 T N N ? 2 U N N ? 2 V N N ? 2 W N N ? 2 X N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order covale ? covale1 A NZ LYS 240 C LYS 240 1_555 M C4A PLP . C PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale2 B NZ LYS 240 A LYS 240 1_555 N C4A PLP . A PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale3 C NZ LYS 240 B LYS 240 1_555 O C4A PLP . B PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale4 D NZ LYS 240 D LYS 240 1_555 P C4A PLP . D PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale5 E NZ LYS 240 E LYS 240 1_555 Q C4A PLP . E PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale6 F NZ LYS 240 F LYS 240 1_555 R C4A PLP . F PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale7 G NZ LYS 240 G LYS 240 1_555 S C4A PLP . G PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale8 H NZ LYS 240 H LYS 240 1_555 T C4A PLP . H PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale9 I NZ LYS 240 I LYS 240 1_555 U C4A PLP . I PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale10 J NZ LYS 240 J LYS 240 1_555 V C4A PLP . J PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale11 K NZ LYS 240 K LYS 240 1_555 W C4A PLP . K PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale12 L NZ LYS 240 L LYS 240 1_555 X C4A PLP . L PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? # _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 5Z0Q _atom_sites.fract_transf_matrix[1][1] 0.017205 _atom_sites.fract_transf_matrix[1][2] -0.001035 _atom_sites.fract_transf_matrix[1][3] -0.001627 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007499 _atom_sites.fract_transf_matrix[2][3] -0.000038 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.006062 _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 M 2 PLP C 1 401 666 PLP PLP . N 2 PLP A 1 401 666 PLP PLP . O 2 PLP B 1 401 666 PLP PLP . P 2 PLP D 1 401 666 PLP PLP . Q 2 PLP E 1 401 666 PLP PLP . R 2 PLP F 1 401 666 PLP PLP . S 2 PLP G 1 401 666 PLP PLP . T 2 PLP H 1 401 666 PLP PLP . U 2 PLP I 1 401 666 PLP PLP . V 2 PLP J 1 401 666 PLP PLP . W 2 PLP K 1 401 666 PLP PLP . X 2 PLP L 1 401 666 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 . . . M 2 149.696 -104.017 86.508 1 34 ? N1 PLP 401 C 1 HETATM 2 C C2 PLP . . . M 2 148.577 -103.824 85.722 1 34.69 ? C2 PLP 401 C 1 HETATM 3 C C2A PLP . . . M 2 148.649 -104.062 84.242 1 34.89 ? C2A PLP 401 C 1 HETATM 4 C C3 PLP . . . M 2 147.382 -103.414 86.301 1 36.53 ? C3 PLP 401 C 1 HETATM 5 O O3 PLP . . . M 2 146.272 -103.223 85.521 1 36.52 ? O3 PLP 401 C 1 HETATM 6 C C4 PLP . . . M 2 147.315 -103.196 87.673 1 42.98 ? C4 PLP 401 C 1 HETATM 7 C C4A PLP . . . M 2 145.992 -102.925 88.326 1 41.52 ? C4A PLP 401 C 1 HETATM 8 C C5 PLP . . . M 2 148.446 -103.388 88.458 1 44.62 ? C5 PLP 401 C 1 HETATM 9 C C6 PLP . . . M 2 149.636 -103.801 87.87 1 39.34 ? C6 PLP 401 C 1 HETATM 10 C C5A PLP . . . M 2 148.362 -103.149 89.949 1 45.84 ? C5A PLP 401 C 1 HETATM 11 O O4P PLP . . . M 2 149.635 -102.878 90.491 1 42.8 ? O4P PLP 401 C 1 HETATM 12 P P PLP . . . M 2 149.751 -102.317 91.996 1 47.94 ? P PLP 401 C 1 HETATM 13 O O1P PLP . . . M 2 148.811 -101.147 92.169 1 46.57 ? O1P PLP 401 C 1 HETATM 14 O O2P PLP . . . M 2 151.168 -101.87 92.272 1 41.25 ? O2P PLP 401 C 1 HETATM 15 O O3P PLP . . . M 2 149.37 -103.424 92.95 1 44.89 ? O3P PLP 401 C 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 42 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 15 #