data_3RCH # _model_server_result.job_id x0ATBhZEmGQs-Y4N3tbhxQ _model_server_result.datetime_utc '2024-11-04 05:05:03' _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 3rch # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":481}' # _entry.id 3RCH # _exptl.entry_id 3RCH _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 90 _cell.entry_id 3RCH _cell.length_a 177 _cell.length_b 177 _cell.length_c 74.83 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RCH _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 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 _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 C _struct_conn.ptnr1_label_comp_id LLP _struct_conn.ptnr1_label_seq_id 303 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LLP _struct_conn.ptnr1_auth_seq_id 303 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id N _struct_conn.ptnr2_label_comp_id TRP _struct_conn.ptnr2_label_seq_id 304 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id TRP _struct_conn.ptnr2_auth_seq_id 304 _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 1.326 _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 307 n y N1 C6 PLP sing 308 n y C2 C2A PLP sing 309 n n C2 C3 PLP sing 310 n y C2A H2A1 PLP sing 311 n n C2A H2A2 PLP sing 312 n n C2A H2A3 PLP sing 313 n n C3 O3 PLP sing 314 n n C3 C4 PLP doub 315 n y O3 HO3 PLP sing 316 n n C4 C4A PLP sing 317 n n C4 C5 PLP sing 318 n y C4A O4A PLP doub 319 n n C4A H4A PLP sing 320 n n C5 C6 PLP doub 321 n y C5 C5A PLP sing 322 n n C6 H6 PLP sing 323 n n C5A O4P PLP sing 324 n n C5A H5A1 PLP sing 325 n n C5A H5A2 PLP sing 326 n n O4P P PLP sing 327 n n P O1P PLP doub 328 n n P O2P PLP sing 329 n n P O3P PLP sing 330 n n O2P HOP2 PLP sing 331 n n O3P HOP3 PLP sing 332 n n # _atom_sites.entry_id 3RCH _atom_sites.fract_transf_matrix[1][1] 0.00565 _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] 0.00565 _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] 0.013364 _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 3 PLP B 1 481 1 PLP PLP . D 4 HOH A 1 481 1 HOH HOH . D 4 HOH A 2 482 4 HOH HOH . D 4 HOH A 3 483 5 HOH HOH . D 4 HOH A 4 484 11 HOH HOH . D 4 HOH A 5 485 12 HOH HOH . D 4 HOH A 6 486 14 HOH HOH . D 4 HOH A 7 487 15 HOH HOH . D 4 HOH A 8 488 17 HOH HOH . D 4 HOH A 9 489 18 HOH HOH . D 4 HOH A 10 490 20 HOH HOH . D 4 HOH A 11 491 22 HOH HOH . D 4 HOH A 12 492 23 HOH HOH . D 4 HOH A 13 493 25 HOH HOH . D 4 HOH A 14 494 27 HOH HOH . E 4 HOH B 1 482 2 HOH HOH . E 4 HOH B 2 483 3 HOH HOH . E 4 HOH B 3 484 6 HOH HOH . E 4 HOH B 4 485 7 HOH HOH . E 4 HOH B 5 486 8 HOH HOH . E 4 HOH B 6 487 9 HOH HOH . E 4 HOH B 7 488 10 HOH HOH . E 4 HOH B 8 489 13 HOH HOH . E 4 HOH B 9 490 16 HOH HOH . E 4 HOH B 10 491 19 HOH HOH . E 4 HOH B 11 492 21 HOH HOH . E 4 HOH B 12 493 24 HOH HOH . E 4 HOH B 13 494 26 HOH HOH . E 4 HOH B 14 495 28 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 . . . C 3 43.576 13.743 -13.231 0.5 32.92 ? N1 PLP 481 B 1 HETATM 2 C C2 PLP . . . C 3 44.418 12.901 -13.924 0.5 33.36 ? C2 PLP 481 B 1 HETATM 3 C C2A PLP . . . C 3 43.999 12.418 -15.281 0.5 32.18 ? C2A PLP 481 B 1 HETATM 4 C C3 PLP . . . C 3 45.636 12.518 -13.358 0.5 34.77 ? C3 PLP 481 B 1 HETATM 5 O O3 PLP . . . C 3 46.512 11.685 -14.006 0.5 33.77 ? O3 PLP 481 B 1 HETATM 6 C C4 PLP . . . C 3 45.987 12.973 -12.098 0.5 35.88 ? C4 PLP 481 B 1 HETATM 7 C C4A PLP . . . C 3 47.405 12.806 -11.622 0.5 39.31 ? C4A PLP 481 B 1 HETATM 8 O O4A PLP . . . C 3 47.792 11.735 -11.13 0.5 41.68 ? O4A PLP 481 B 1 HETATM 9 C C5 PLP . . . C 3 45.125 13.813 -11.417 0.5 34.24 ? C5 PLP 481 B 1 HETATM 10 C C6 PLP . . . C 3 43.917 14.199 -11.978 0.5 32.94 ? C6 PLP 481 B 1 HETATM 11 C C5A PLP . . . C 3 45.515 14.302 -10.052 0.5 34.21 ? C5A PLP 481 B 1 HETATM 12 O O4P PLP . . . C 3 46.623 15.157 -10.139 0.5 33.7 ? O4P PLP 481 B 1 HETATM 13 P P PLP . . . C 3 47.065 15.879 -8.778 0.5 35.51 ? P PLP 481 B 1 HETATM 14 O O1P PLP . . . C 3 47.587 14.78 -7.887 0.5 36.34 ? O1P PLP 481 B 1 HETATM 15 O O2P PLP . . . C 3 45.888 16.517 -8.066 0.5 33.57 ? O2P PLP 481 B 1 HETATM 16 O O3P PLP . . . C 3 48.153 16.887 -9.075 0.5 33.35 ? O3P PLP 481 B 1 # _model_server_stats.io_time_ms 125 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 16 #