data_6XWL # _model_server_result.job_id VW7eV7WxkGiti52sYFUYsg _model_server_result.datetime_utc '2025-04-27 01:08:25' _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 6xwl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":601}' # _entry.id 6XWL # _exptl.entry_id 6XWL _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 6 _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 6XWL _cell.length_a 83.237 _cell.length_b 83.237 _cell.length_c 420.309 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XWL _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,H 1 1 C,E,I,K 2 1 D,F,J,L 3 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 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L 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 56 F LYS 56 1_555 G C4A PLP . F PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? covale ? covale2 B NZ LYS 56 A LYS 56 1_555 H C4A PLP . A PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.51 ? covale ? covale3 C NZ LYS 56 B LYS 56 1_555 I C4A PLP . B PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.478 ? covale ? covale4 D NZ LYS 56 C LYS 56 1_555 J C4A PLP . C PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale5 E NZ LYS 56 D LYS 56 1_555 K C4A PLP . D PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.484 ? covale ? covale6 F NZ LYS 56 E LYS 56 1_555 L C4A PLP . E PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.496 ? # _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 6XWL _atom_sites.fract_transf_matrix[1][1] 0.012014 _atom_sites.fract_transf_matrix[1][2] 0.006936 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013872 _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] 0.002379 _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 G 2 PLP F 1 601 1551 PLP PLP . H 2 PLP A 1 601 1551 PLP PLP . I 2 PLP B 1 601 1551 PLP PLP . J 2 PLP C 1 601 1551 PLP PLP . K 2 PLP D 1 601 1551 PLP PLP . L 2 PLP E 1 601 1551 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 . . . L 2 17.482 0.649 106.944 1 107.04 ? N1 PLP 601 E 1 HETATM 2 C C2 PLP . . . L 2 17.752 1.749 106.248 1 105.44 ? C2 PLP 601 E 1 HETATM 3 C C2A PLP . . . L 2 18.773 1.681 105.16 1 104.25 ? C2A PLP 601 E 1 HETATM 4 C C3 PLP . . . L 2 17.092 2.95 106.532 1 105.08 ? C3 PLP 601 E 1 HETATM 5 O O3 PLP . . . L 2 17.407 4.041 105.795 1 103.62 ? O3 PLP 601 E 1 HETATM 6 C C4 PLP . . . L 2 16.13 2.998 107.561 1 106.25 ? C4 PLP 601 E 1 HETATM 7 C C4A PLP . . . L 2 15.47 4.278 107.833 1 106.04 ? C4A PLP 601 E 1 HETATM 8 C C5 PLP . . . L 2 15.877 1.818 108.288 1 107.99 ? C5 PLP 601 E 1 HETATM 9 C C6 PLP . . . L 2 16.564 0.69 107.931 1 108.41 ? C6 PLP 601 E 1 HETATM 10 C C5A PLP . . . L 2 14.869 1.713 109.403 1 109.65 ? C5A PLP 601 E 1 HETATM 11 O O4P PLP . . . L 2 13.946 2.837 109.549 1 108.6 ? O4P PLP 601 E 1 HETATM 12 P P PLP . . . L 2 12.741 2.789 110.618 1 110.06 ? P PLP 601 E 1 HETATM 13 O O1P PLP . . . L 2 11.708 3.787 110.13 1 108.52 ? O1P PLP 601 E 1 HETATM 14 O O2P PLP . . . L 2 13.343 3.163 111.956 1 110.87 ? O2P PLP 601 E 1 HETATM 15 O O3P PLP . . . L 2 12.246 1.358 110.587 1 111.37 ? O3P PLP 601 E 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 15 #