data_9GPB # _model_server_result.job_id viGUdFSU0z22gfWMYUp7Cg _model_server_result.datetime_utc '2024-10-13 19:15:57' _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 9gpb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":999}' # _entry.id 9GPB # _exptl.entry_id 9GPB _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 109.35 _cell.angle_gamma 90 _cell.entry_id 9GPB _cell.length_a 119 _cell.length_b 190 _cell.length_c 88.2 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9GPB _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _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,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T _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 H N N ? 3 L N N ? 3 P N N ? 3 T 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 A NZ LYS 680 A LYS 680 1_555 H C4A PLP . A PLP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale2 B CD ARG 569 B ARG 569 1_555 J O4 SO4 . B SO4 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? covale ? covale3 B NE ARG 569 B ARG 569 1_555 J O4 SO4 . B SO4 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.287 ? covale ? covale4 B NZ LYS 680 B LYS 680 1_555 L C4A PLP . B PLP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.365 ? covale ? covale5 C NZ LYS 680 C LYS 680 1_555 P C4A PLP . C PLP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.364 ? covale ? covale6 D NH2 ARG 43 D ARG 43 1_555 M O3 SO4 . C SO4 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.795 ? covale ? covale7 D NZ LYS 680 D LYS 680 1_555 T C4A PLP . D PLP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.363 ? # _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' # _atom_sites.entry_id 9GPB _atom_sites.fract_transf_matrix[1][1] 0.008403 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002951 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005263 _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] 0.012017 _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 E 2 SO4 A 1 900 900 SO4 SO4 . F 2 SO4 A 1 901 901 SO4 SO4 . G 2 SO4 A 1 902 902 SO4 SO4 . H 3 PLP A 1 999 999 PLP PLP . I 2 SO4 B 1 900 900 SO4 SO4 . J 2 SO4 B 1 901 901 SO4 SO4 . K 2 SO4 B 1 902 902 SO4 SO4 . L 3 PLP B 1 999 999 PLP PLP . M 2 SO4 C 1 900 900 SO4 SO4 . N 2 SO4 C 1 901 901 SO4 SO4 . O 2 SO4 C 1 902 902 SO4 SO4 . P 3 PLP C 1 999 999 PLP PLP . Q 2 SO4 D 1 900 900 SO4 SO4 . R 2 SO4 D 1 901 901 SO4 SO4 . S 2 SO4 D 1 902 902 SO4 SO4 . T 3 PLP D 1 999 999 PLP PLP . # 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 . . . L 3 84.958 -1.673 68.727 1 10.29 ? N1 PLP 999 B 1 HETATM 2 C C2 PLP . . . L 3 84.299 -2.872 68.856 1 11.27 ? C2 PLP 999 B 1 HETATM 3 C C2A PLP . . . L 3 84.163 -3.764 67.658 1 9.3 ? C2A PLP 999 B 1 HETATM 4 C C3 PLP . . . L 3 83.942 -3.354 70.095 1 8.18 ? C3 PLP 999 B 1 HETATM 5 O O3 PLP . . . L 3 83.182 -4.517 70.144 1 7.65 ? O3 PLP 999 B 1 HETATM 6 C C4 PLP . . . L 3 84.29 -2.647 71.239 1 5.82 ? C4 PLP 999 B 1 HETATM 7 C C4A PLP . . . L 3 83.879 -3.108 72.598 1 8 ? C4A PLP 999 B 1 HETATM 8 C C5 PLP . . . L 3 84.998 -1.475 71.105 1 7.84 ? C5 PLP 999 B 1 HETATM 9 C C6 PLP . . . L 3 85.312 -0.988 69.855 1 10.88 ? C6 PLP 999 B 1 HETATM 10 C C5A PLP . . . L 3 85.483 -0.747 72.3 1 10.46 ? C5A PLP 999 B 1 HETATM 11 O O4P PLP . . . L 3 86.836 -0.195 72.292 1 8.83 ? O4P PLP 999 B 1 HETATM 12 P P PLP . . . L 3 87.478 0.21 73.677 1 7.22 ? P PLP 999 B 1 HETATM 13 O O1P PLP . . . L 3 86.397 0.597 74.591 1 12.82 ? O1P PLP 999 B 1 HETATM 14 O O2P PLP . . . L 3 88.094 -1.042 74.079 1 6.2 ? O2P PLP 999 B 1 HETATM 15 O O3P PLP . . . L 3 88.423 1.316 73.378 1 16.65 ? O3P PLP 999 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 26 _model_server_stats.element_count 15 #