data_5WKP # _model_server_result.job_id ivQTen7UWCHGTkX1rL2WHQ _model_server_result.datetime_utc '2024-11-05 08:31:38' _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 5wkp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":501}' # _entry.id 5WKP # _exptl.entry_id 5WKP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 5WKP _cell.length_a 98.36 _cell.length_b 123.29 _cell.length_c 151.724 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WKP _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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,E,F,G,H,I,J,K,L _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 ? 5 I N N ? 5 K 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 207 A LYS 258 1_555 I C4A PLP . A PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale2 C OG SER 36 C SER 36 1_555 J P24 8Q1 . C 8Q1 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.56 ? covale ? covale3 E NZ LYS 207 E LYS 258 1_555 K C4A PLP . E PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale4 G OG SER 36 G SER 36 1_555 L P24 8Q1 . G 8Q1 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.56 ? # _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 337 n y N1 C6 PLP sing 338 n y C2 C2A PLP sing 339 n n C2 C3 PLP sing 340 n y C2A H2A1 PLP sing 341 n n C2A H2A2 PLP sing 342 n n C2A H2A3 PLP sing 343 n n C3 O3 PLP sing 344 n n C3 C4 PLP doub 345 n y O3 HO3 PLP sing 346 n n C4 C4A PLP sing 347 n n C4 C5 PLP sing 348 n y C4A O4A PLP doub 349 n n C4A H4A PLP sing 350 n n C5 C6 PLP doub 351 n y C5 C5A PLP sing 352 n n C6 H6 PLP sing 353 n n C5A O4P PLP sing 354 n n C5A H5A1 PLP sing 355 n n C5A H5A2 PLP sing 356 n n O4P P PLP sing 357 n n P O1P PLP doub 358 n n P O2P PLP sing 359 n n P O3P PLP sing 360 n n O2P HOP2 PLP sing 361 n n O3P HOP3 PLP sing 362 n n # _atom_sites.entry_id 5WKP _atom_sites.fract_transf_matrix[1][1] 0.010167 _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] 0.008111 _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] 0.006591 _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 I 5 PLP A 1 501 460 PLP PLP . J 6 8Q1 C 1 301 301 8Q1 PM8 . K 5 PLP E 1 501 460 PLP PLP . L 6 8Q1 G 1 301 301 8Q1 PM8 . # 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 . . . I 5 45.169 41.143 56.358 1 74.9 ? N1 PLP 501 A 1 HETATM 2 C C2 PLP . . . I 5 44.845 39.845 56.168 1 77.58 ? C2 PLP 501 A 1 HETATM 3 C C2A PLP . . . I 5 45.524 39.033 55.074 1 73.09 ? C2A PLP 501 A 1 HETATM 4 C C3 PLP . . . I 5 43.89 39.237 56.965 1 88.89 ? C3 PLP 501 A 1 HETATM 5 O O3 PLP . . . I 5 43.563 37.892 56.755 1 92.7 ? O3 PLP 501 A 1 HETATM 6 C C4 PLP . . . I 5 43.276 39.942 57.945 1 89.43 ? C4 PLP 501 A 1 HETATM 7 C C4A PLP . . . I 5 42.22 39.258 58.817 1 87.14 ? C4A PLP 501 A 1 HETATM 8 C C5 PLP . . . I 5 43.604 41.245 58.14 1 85.43 ? C5 PLP 501 A 1 HETATM 9 C C6 PLP . . . I 5 44.556 41.849 57.336 1 80.35 ? C6 PLP 501 A 1 HETATM 10 C C5A PLP . . . I 5 42.925 42.077 59.226 1 80.3 ? C5A PLP 501 A 1 HETATM 11 O O4P PLP . . . I 5 43.803 42.403 60.255 1 71.37 ? O4P PLP 501 A 1 HETATM 12 P P PLP . . . I 5 43.182 43.598 61.19 1 78.61 ? P PLP 501 A 1 HETATM 13 O O1P PLP . . . I 5 43.407 44.916 60.488 1 81.63 ? O1P PLP 501 A 1 HETATM 14 O O2P PLP . . . I 5 43.808 43.616 62.562 1 92.31 ? O2P PLP 501 A 1 HETATM 15 O O3P PLP . . . I 5 41.699 43.341 61.31 1 79.14 ? O3P PLP 501 A 1 HETATM 16 H H2A1 PLP . . . I 5 45.94 38.249 55.465 1 88.19 ? H2A1 PLP 501 A 1 HETATM 17 H H2A2 PLP . . . I 5 46.202 39.577 54.642 1 88.19 ? H2A2 PLP 501 A 1 HETATM 18 H H2A3 PLP . . . I 5 44.865 38.757 54.419 1 88.19 ? H2A3 PLP 501 A 1 HETATM 19 H H6 PLP . . . I 5 44.777 42.742 57.47 1 96.9 ? H6 PLP 501 A 1 HETATM 20 H H5A1 PLP . . . I 5 42.585 42.895 58.83 1 96.84 ? H5A1 PLP 501 A 1 HETATM 21 H H5A2 PLP . . . I 5 42.183 41.571 59.592 1 96.84 ? H5A2 PLP 501 A 1 # _model_server_stats.io_time_ms 115 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #