data_8IRZ # _model_server_result.job_id PgripiALg5ySx_l1F5hDFA _model_server_result.datetime_utc '2024-11-01 14:33:06' _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 8irz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":400}' # _entry.id 8IRZ # _exptl.entry_id 8IRZ _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 125.82 _cell.angle_gamma 90 _cell.entry_id 8IRZ _cell.length_a 108.966 _cell.length_b 174.395 _cell.length_c 84.089 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8IRZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1,2 B,D,F 2 1,3 # 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' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 3 'crystal symmetry operation' 2_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -49.21231 0 68.184371 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N 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 224 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 203 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _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 400 _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 1.293 _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 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 8IRZ _atom_sites.fract_transf_matrix[1][1] 0.009177 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006624 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005734 _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] 0.014666 _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 PLP A 1 400 400 PLP PLP . D 2 PLP B 1 400 400 PLP PLP . E 3 HOH A 1 501 91 HOH HOH . E 3 HOH A 2 502 15 HOH HOH . E 3 HOH A 3 503 27 HOH HOH . E 3 HOH A 4 504 62 HOH HOH . E 3 HOH A 5 505 58 HOH HOH . E 3 HOH A 6 506 46 HOH HOH . E 3 HOH A 7 507 90 HOH HOH . E 3 HOH A 8 508 12 HOH HOH . E 3 HOH A 9 509 10 HOH HOH . E 3 HOH A 10 510 89 HOH HOH . F 3 HOH B 1 501 65 HOH HOH . F 3 HOH B 2 502 39 HOH HOH . F 3 HOH B 3 503 22 HOH HOH . F 3 HOH B 4 504 76 HOH HOH . F 3 HOH B 5 505 68 HOH HOH . F 3 HOH B 6 506 28 HOH HOH . F 3 HOH B 7 507 45 HOH HOH . F 3 HOH B 8 508 18 HOH HOH . F 3 HOH B 9 509 43 HOH HOH . F 3 HOH B 10 510 9 HOH HOH . F 3 HOH B 11 511 13 HOH HOH . # 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 2 -8.909 5.807 36.689 1 66.27 ? N1 PLP 400 B 1 HETATM 2 C C2 PLP . . . D 2 -8.015 4.952 36.197 1 68.38 ? C2 PLP 400 B 1 HETATM 3 C C2A PLP . . . D 2 -6.612 5.04 36.704 1 68.97 ? C2A PLP 400 B 1 HETATM 4 C C3 PLP . . . D 2 -8.389 4.001 35.224 1 70.67 ? C3 PLP 400 B 1 HETATM 5 O O3 PLP . . . D 2 -7.519 3.088 34.662 1 77.53 ? O3 PLP 400 B 1 HETATM 6 C C4 PLP . . . D 2 -9.727 3.963 34.786 1 67.05 ? C4 PLP 400 B 1 HETATM 7 C C4A PLP . . . D 2 -10.128 2.993 33.764 1 70.86 ? C4A PLP 400 B 1 HETATM 8 C C5 PLP . . . D 2 -10.639 4.881 35.328 1 64.54 ? C5 PLP 400 B 1 HETATM 9 C C6 PLP . . . D 2 -10.188 5.772 36.261 1 63.9 ? C6 PLP 400 B 1 HETATM 10 C C5A PLP . . . D 2 -12.075 4.914 34.891 1 65.15 ? C5A PLP 400 B 1 HETATM 11 O O4P PLP . . . D 2 -12.682 3.602 35.078 1 60.35 ? O4P PLP 400 B 1 HETATM 12 P P PLP . . . D 2 -14.165 3.279 34.565 1 69.37 ? P PLP 400 B 1 HETATM 13 O O1P PLP . . . D 2 -13.924 2.867 33.117 1 69.59 ? O1P PLP 400 B 1 HETATM 14 O O2P PLP . . . D 2 -15.036 4.53 34.709 1 58.2 ? O2P PLP 400 B 1 HETATM 15 O O3P PLP . . . D 2 -14.641 2.138 35.467 1 74.87 ? O3P PLP 400 B 1 # _model_server_stats.io_time_ms 78 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 15 #