data_8GKZ # _model_server_result.job_id bnShwDYbz3cQAKGXxIs5sQ _model_server_result.datetime_utc '2024-10-10 11:19:50' _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 8gkz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":603}' # _entry.id 8GKZ # _exptl.entry_id 8GKZ _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 2 _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 8GKZ _cell.length_a 158.25 _cell.length_b 158.25 _cell.length_c 207.99 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GKZ _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 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 _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' 12_564 x,x-y+1,-z-1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -79.125 137.04852 -34.665 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 G 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 269 A LYS 280 1_555 D C4A PLP . A PLP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 B NZ LYS 269 B LYS 280 1_555 G C4A PLP . B PLP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? # _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 8GKZ _atom_sites.fract_transf_matrix[1][1] 0.006319 _atom_sites.fract_transf_matrix[1][2] 0.003648 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007297 _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] 0.004808 _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 GLY A 1 601 602 GLY GLY . D 3 PLP A 1 602 280 PLP LLP . E 4 Y72 B 1 601 601 Y72 G62 . F 2 GLY B 1 602 601 GLY GLY . G 3 PLP B 1 603 280 PLP LLP . H 5 HOH A 1 701 13 HOH HOH . H 5 HOH A 2 702 21 HOH HOH . H 5 HOH A 3 703 14 HOH HOH . H 5 HOH A 4 704 15 HOH HOH . H 5 HOH A 5 705 20 HOH HOH . H 5 HOH A 6 706 8 HOH HOH . H 5 HOH A 7 707 19 HOH HOH . H 5 HOH A 8 708 5 HOH HOH . H 5 HOH A 9 709 9 HOH HOH . H 5 HOH A 10 710 6 HOH HOH . H 5 HOH A 11 711 18 HOH HOH . H 5 HOH A 12 712 7 HOH HOH . H 5 HOH A 13 713 23 HOH HOH . H 5 HOH A 14 714 16 HOH HOH . H 5 HOH A 15 715 12 HOH HOH . I 5 HOH B 1 701 11 HOH HOH . I 5 HOH B 2 702 1 HOH HOH . I 5 HOH B 3 703 22 HOH HOH . I 5 HOH B 4 704 10 HOH HOH . I 5 HOH B 5 705 17 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 . . . G 3 -8.978 74.867 1.943 1 44.78 ? N1 PLP 603 B 1 HETATM 2 C C2 PLP . . . G 3 -7.768 74.956 2.493 1 46.24 ? C2 PLP 603 B 1 HETATM 3 C C2A PLP . . . G 3 -6.971 76.291 2.413 1 38.58 ? C2A PLP 603 B 1 HETATM 4 C C3 PLP . . . G 3 -7.208 73.83 3.152 1 51.66 ? C3 PLP 603 B 1 HETATM 5 O O3 PLP . . . G 3 -5.941 73.925 3.731 1 61 ? O3 PLP 603 B 1 HETATM 6 C C4 PLP . . . G 3 -7.899 72.645 3.237 1 49.37 ? C4 PLP 603 B 1 HETATM 7 C C4A PLP . . . G 3 -7.186 71.415 4.006 1 43.64 ? C4A PLP 603 B 1 HETATM 8 C C5 PLP . . . G 3 -9.143 72.55 2.674 1 36.59 ? C5 PLP 603 B 1 HETATM 9 C C6 PLP . . . G 3 -9.688 73.664 2.019 1 41.55 ? C6 PLP 603 B 1 HETATM 10 C C5A PLP . . . G 3 -10 71.243 2.692 1 31.2 ? C5A PLP 603 B 1 HETATM 11 O O4P PLP . . . G 3 -10.2 70.684 3.965 1 41.36 ? O4P PLP 603 B 1 HETATM 12 P P PLP . . . G 3 -10.88 69.299 3.989 1 41.41 ? P PLP 603 B 1 HETATM 13 O O1P PLP . . . G 3 -12.118 69.349 3.162 1 42.89 ? O1P PLP 603 B 1 HETATM 14 O O2P PLP . . . G 3 -11.211 68.943 5.386 1 46.58 ? O2P PLP 603 B 1 HETATM 15 O O3P PLP . . . G 3 -9.935 68.245 3.392 1 41.07 ? O3P PLP 603 B 1 # _model_server_stats.io_time_ms 71 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #