data_2DH5 # _model_server_result.job_id Cpw7da7wHHoOHr9-C_tKWw _model_server_result.datetime_utc '2024-11-16 22:44:26' _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 2dh5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 2DH5 # _exptl.entry_id 2DH5 _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 1 _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 2DH5 _cell.length_a 172.516 _cell.length_b 172.516 _cell.length_c 82.587 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2DH5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 11_655 -x+y+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 172.516 0 41.2935 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 87 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 87 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id D _struct_conn.ptnr2_label_atom_id C4A _struct_conn.ptnr2_label_comp_id PLP _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id PLP _struct_conn.ptnr2_auth_seq_id 501 _struct_conn.ptnr2_symmetry 1_555 _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 1.291 _struct_conn.pdbx_value_order ? # _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 273 n y N1 C6 PLP sing 274 n y C2 C2A PLP sing 275 n n C2 C3 PLP sing 276 n y C2A H2A1 PLP sing 277 n n C2A H2A2 PLP sing 278 n n C2A H2A3 PLP sing 279 n n C3 O3 PLP sing 280 n n C3 C4 PLP doub 281 n y O3 HO3 PLP sing 282 n n C4 C4A PLP sing 283 n n C4 C5 PLP sing 284 n y C4A O4A PLP doub 285 n n C4A H4A PLP sing 286 n n C5 C6 PLP doub 287 n y C5 C5A PLP sing 288 n n C6 H6 PLP sing 289 n n C5A O4P PLP sing 290 n n C5A H5A1 PLP sing 291 n n C5A H5A2 PLP sing 292 n n O4P P PLP sing 293 n n P O1P PLP doub 294 n n P O2P PLP sing 295 n n P O3P PLP sing 296 n n O2P HOP2 PLP sing 297 n n O3P HOP3 PLP sing 298 n n # _atom_sites.entry_id 2DH5 _atom_sites.fract_transf_matrix[1][1] 0.005797 _atom_sites.fract_transf_matrix[1][2] 0.003347 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006693 _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] 0.012108 _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 B 2 SO4 A 1 801 801 SO4 SO4 . C 2 SO4 A 1 802 802 SO4 SO4 . D 3 PLP A 1 501 501 PLP PLP . E 4 GOL A 1 901 901 GOL GOL . F 5 HOH A 1 902 1001 HOH WAT . F 5 HOH A 2 903 1002 HOH WAT . F 5 HOH A 3 904 1003 HOH WAT . F 5 HOH A 4 905 1004 HOH WAT . F 5 HOH A 5 906 1005 HOH WAT . F 5 HOH A 6 907 1006 HOH WAT . F 5 HOH A 7 908 1007 HOH WAT . F 5 HOH A 8 909 1008 HOH WAT . F 5 HOH A 9 910 1009 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 3 100.08 15.123 22.291 1 39.5 ? N1 PLP 501 A 1 HETATM 2 C C2 PLP . . . D 3 99.01 14.644 21.544 1 37.5 ? C2 PLP 501 A 1 HETATM 3 C C2A PLP . . . D 3 97.691 14.562 22.211 1 33.82 ? C2A PLP 501 A 1 HETATM 4 C C3 PLP . . . D 3 99.301 14.089 20.249 1 38.63 ? C3 PLP 501 A 1 HETATM 5 O O3 PLP . . . D 3 98.259 13.482 19.533 1 43.1 ? O3 PLP 501 A 1 HETATM 6 C C4 PLP . . . D 3 100.608 13.993 19.808 1 38.66 ? C4 PLP 501 A 1 HETATM 7 C C4A PLP . . . D 3 100.744 13.354 18.501 1 43.78 ? C4A PLP 501 A 1 HETATM 8 C C5 PLP . . . D 3 101.672 14.442 20.563 1 41.07 ? C5 PLP 501 A 1 HETATM 9 C C6 PLP . . . D 3 101.405 15.08 21.838 1 43.06 ? C6 PLP 501 A 1 HETATM 10 C C5A PLP . . . D 3 103.135 14.183 20.372 1 44.49 ? C5A PLP 501 A 1 HETATM 11 O O4P PLP . . . D 3 103.677 15.065 19.357 1 50.6 ? O4P PLP 501 A 1 HETATM 12 P P PLP . . . D 3 104.463 16.306 19.442 1 46.91 ? P PLP 501 A 1 HETATM 13 O O1P PLP . . . D 3 105.618 16.255 20.582 1 46.4 ? O1P PLP 501 A 1 HETATM 14 O O2P PLP . . . D 3 103.324 17.375 19.739 1 45.07 ? O2P PLP 501 A 1 HETATM 15 O O3P PLP . . . D 3 105.066 16.305 17.947 1 47.37 ? O3P PLP 501 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 15 #