data_1GCK # _model_server_result.job_id XiH7bDLShvl3mNxZFIOT_A _model_server_result.datetime_utc '2024-10-19 14:45:33' _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 1gck # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":413}' # _entry.id 1GCK # _exptl.entry_id 1GCK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 3 _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 1GCK _cell.length_a 62.75 _cell.length_b 74.89 _cell.length_c 163.9 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1GCK _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 3 D N N ? 3 F 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 D C4A PLP . A PLP 413 1_555 C N ASP . A ASP 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.511 ? covale ? covale2 F C4A PLP . B PLP 913 1_555 E N ASP . B ASP 914 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? # _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 260 n y N1 C6 PLP sing 261 n y C2 C2A PLP sing 262 n n C2 C3 PLP sing 263 n y C2A H2A1 PLP sing 264 n n C2A H2A2 PLP sing 265 n n C2A H2A3 PLP sing 266 n n C3 O3 PLP sing 267 n n C3 C4 PLP doub 268 n y O3 HO3 PLP sing 269 n n C4 C4A PLP sing 270 n n C4 C5 PLP sing 271 n y C4A O4A PLP doub 272 n n C4A H4A PLP sing 273 n n C5 C6 PLP doub 274 n y C5 C5A PLP sing 275 n n C6 H6 PLP sing 276 n n C5A O4P PLP sing 277 n n C5A H5A1 PLP sing 278 n n C5A H5A2 PLP sing 279 n n O4P P PLP sing 280 n n P O1P PLP doub 281 n n P O2P PLP sing 282 n n P O3P PLP sing 283 n n O2P HOP2 PLP sing 284 n n O3P HOP3 PLP sing 285 n n # _atom_sites.entry_id 1GCK _atom_sites.fract_transf_matrix[1][1] 0.015936 _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] 0.013353 _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] 0.006101 _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 C 2 ASP A 1 414 414 ASP ASP . D 3 PLP A 1 413 413 PLP PLP . E 2 ASP B 1 914 914 ASP ASP . F 3 PLP B 1 913 913 PLP PLP . G 4 HOH A 1 1005 1005 HOH WAT . G 4 HOH A 2 1007 1007 HOH WAT . G 4 HOH A 3 1008 1008 HOH WAT . G 4 HOH A 4 1010 1010 HOH WAT . G 4 HOH A 5 1012 1012 HOH WAT . G 4 HOH A 6 1013 1013 HOH WAT . G 4 HOH A 7 1014 1014 HOH WAT . G 4 HOH A 8 1019 1019 HOH WAT . G 4 HOH A 9 1020 1020 HOH WAT . H 4 HOH B 1 1001 1001 HOH WAT . H 4 HOH B 2 1002 1002 HOH WAT . H 4 HOH B 3 1003 1003 HOH WAT . H 4 HOH B 4 1004 1004 HOH WAT . H 4 HOH B 5 1006 1006 HOH WAT . H 4 HOH B 6 1009 1009 HOH WAT . H 4 HOH B 7 1011 1011 HOH WAT . H 4 HOH B 8 1015 1015 HOH WAT . H 4 HOH B 9 1016 1016 HOH WAT . H 4 HOH B 10 1017 1017 HOH WAT . H 4 HOH B 11 1018 1018 HOH WAT . # 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 . . . D 3 12.445 2.725 57.367 1 32.34 ? N1 PLP 413 A 1 HETATM 2 C C2 PLP . . . D 3 13.588 2.064 57.012 1 35.55 ? C2 PLP 413 A 1 HETATM 3 C C2A PLP . . . D 3 13.583 0.549 57.044 1 38.45 ? C2A PLP 413 A 1 HETATM 4 C C3 PLP . . . D 3 14.691 2.798 56.582 1 37.15 ? C3 PLP 413 A 1 HETATM 5 O O3 PLP . . . D 3 15.734 2.159 56.162 1 41.7 ? O3 PLP 413 A 1 HETATM 6 C C4 PLP . . . D 3 14.675 4.132 56.594 1 38.2 ? C4 PLP 413 A 1 HETATM 7 C C4A PLP . . . D 3 15.526 5.246 55.867 1 40.17 ? C4A PLP 413 A 1 HETATM 8 C C5 PLP . . . D 3 13.45 4.77 56.943 1 37.32 ? C5 PLP 413 A 1 HETATM 9 C C6 PLP . . . D 3 12.388 4.038 57.372 1 31.47 ? C6 PLP 413 A 1 HETATM 10 C C5A PLP . . . D 3 13.359 6.285 57.026 1 34.24 ? C5A PLP 413 A 1 HETATM 11 O O4P PLP . . . D 3 12.702 6.854 55.941 1 38.62 ? O4P PLP 413 A 1 HETATM 12 P P PLP . . . D 3 12.603 8.401 55.533 1 28.32 ? P PLP 413 A 1 HETATM 13 O O1P PLP . . . D 3 11.592 8.382 54.543 1 32.2 ? O1P PLP 413 A 1 HETATM 14 O O2P PLP . . . D 3 13.653 8.739 54.588 1 34.19 ? O2P PLP 413 A 1 HETATM 15 O O3P PLP . . . D 3 12.737 9.315 56.6 1 32.12 ? O3P PLP 413 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 382 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 15 #