data_1XRS # _model_server_result.job_id mT5HIkdJoBJS_aomh0mnRQ _model_server_result.datetime_utc '2025-04-28 22:13:37' _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 1xrs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":801}' # _entry.id 1XRS # _exptl.entry_id 1XRS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 4 _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 1XRS _cell.length_a 99.7 _cell.length_b 99.7 _cell.length_c 168.8 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XRS _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 1,2 # 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' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 168.8 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 B NZ LYS 144 B LYS 144 1_555 D C4A PLP . B PLP 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.394 ? metalc ? metalc1 B NE2 HIS 133 B HIS 133 1_555 C CO B12 . B B12 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? metalc ? metalc2 E C5' 5AD . B 5AD 500 1_555 C CO B12 . B B12 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? # _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 481 n y N1 C6 PLP sing 482 n y C2 C2A PLP sing 483 n n C2 C3 PLP sing 484 n y C2A H2A1 PLP sing 485 n n C2A H2A2 PLP sing 486 n n C2A H2A3 PLP sing 487 n n C3 O3 PLP sing 488 n n C3 C4 PLP doub 489 n y O3 HO3 PLP sing 490 n n C4 C4A PLP sing 491 n n C4 C5 PLP sing 492 n y C4A O4A PLP doub 493 n n C4A H4A PLP sing 494 n n C5 C6 PLP doub 495 n y C5 C5A PLP sing 496 n n C6 H6 PLP sing 497 n n C5A O4P PLP sing 498 n n C5A H5A1 PLP sing 499 n n C5A H5A2 PLP sing 500 n n O4P P PLP sing 501 n n P O1P PLP doub 502 n n P O2P PLP sing 503 n n P O3P PLP sing 504 n n O2P HOP2 PLP sing 505 n n O3P HOP3 PLP sing 506 n n # _atom_sites.entry_id 1XRS _atom_sites.fract_transf_matrix[1][1] 0.01003 _atom_sites.fract_transf_matrix[1][2] 0.005791 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011582 _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] 0.005924 _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 B12 B 1 800 800 B12 B12 . D 4 PLP B 1 801 801 PLP PLP . E 5 5AD B 1 500 500 5AD 5AD . # 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 4 58.957 42.62 81.809 1 29.36 ? N1 PLP 801 B 1 HETATM 2 C C2 PLP . . . D 4 57.675 42.637 81.116 1 25.51 ? C2 PLP 801 B 1 HETATM 3 C C2A PLP . . . D 4 56.862 41.361 81.196 1 23.64 ? C2A PLP 801 B 1 HETATM 4 C C3 PLP . . . D 4 57.277 43.837 80.393 1 26.11 ? C3 PLP 801 B 1 HETATM 5 O O3 PLP . . . D 4 56.068 43.773 79.807 1 33.83 ? O3 PLP 801 B 1 HETATM 6 C C4 PLP . . . D 4 58.087 45.004 80.257 1 25.17 ? C4 PLP 801 B 1 HETATM 7 C C4A PLP . . . D 4 57.619 46.122 79.407 1 22.52 ? C4A PLP 801 B 1 HETATM 8 C C5 PLP . . . D 4 59.493 45.038 80.966 1 28.05 ? C5 PLP 801 B 1 HETATM 9 C C6 PLP . . . D 4 59.859 43.797 81.766 1 25.43 ? C6 PLP 801 B 1 HETATM 10 C C5A PLP . . . D 4 60.555 46.14 80.885 1 25.55 ? C5A PLP 801 B 1 HETATM 11 O O4P PLP . . . D 4 61.41 45.667 79.987 1 27.96 ? O4P PLP 801 B 1 HETATM 12 P P PLP . . . D 4 62.823 45.947 79.643 1 24.08 ? P PLP 801 B 1 HETATM 13 O O1P PLP . . . D 4 62.762 44.852 78.668 1 30.83 ? O1P PLP 801 B 1 HETATM 14 O O2P PLP . . . D 4 63.741 45.715 80.862 1 27.38 ? O2P PLP 801 B 1 HETATM 15 O O3P PLP . . . D 4 62.948 47.223 78.969 1 26.88 ? O3P PLP 801 B 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 15 #