data_5KDE # _model_server_result.job_id cyN-7ceziFXZ2X4rprH6LA _model_server_result.datetime_utc '2024-10-10 01:23:56' _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 5kde # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 5KDE # _exptl.entry_id 5KDE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 175.959 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PYROPHOSPHATE 2-' _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 5KDE _cell.length_a 99.965 _cell.length_b 99.965 _cell.length_c 97.559 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KDE _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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_535 -y,x-y-2,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 99.965 -173.144459 0 3 'crystal symmetry operation' 3_755 -x+y+2,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 199.93 0 0 4 'crystal symmetry operation' 10_557 -y,-x,-z+5/2 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 0 0 243.8975 5 'crystal symmetry operation' 11_757 -x+y+2,y,-z+5/2 -1 0 0 0 1 0 0 0 -1 199.93 0 243.8975 6 'crystal symmetry operation' 12_537 x,x-y-2,-z+5/2 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 99.965 -173.144459 243.8975 # _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 # _chem_comp.formula 'H2 O7 P2 -2' _chem_comp.formula_weight 175.959 _chem_comp.id POP _chem_comp.mon_nstd_flag . _chem_comp.name 'PYROPHOSPHATE 2-' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 P1 O1 POP doub 303 n n P1 O2 POP sing 304 n n P1 O3 POP sing 305 n n P1 O POP sing 306 n n O2 HO2 POP sing 307 n n O P2 POP sing 308 n n P2 O4 POP doub 309 n n P2 O5 POP sing 310 n n P2 O6 POP sing 311 n n O5 HO5 POP sing 312 n n # _atom_sites.entry_id 5KDE _atom_sites.fract_transf_matrix[1][1] 0.010004 _atom_sites.fract_transf_matrix[1][2] 0.005776 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011551 _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] 0.01025 _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 B 2 6RT A 1 201 1 6RT MMI . C 3 POP A 1 202 1 POP POP . D 4 HOH A 1 301 9 HOH HOH . D 4 HOH A 2 302 14 HOH HOH . D 4 HOH A 3 303 7 HOH HOH . D 4 HOH A 4 304 5 HOH HOH . D 4 HOH A 5 305 4 HOH HOH . D 4 HOH A 6 306 8 HOH HOH . D 4 HOH A 7 307 15 HOH HOH . D 4 HOH A 8 308 3 HOH HOH . D 4 HOH A 9 309 9 HOH HOH . D 4 HOH A 10 310 11 HOH HOH . D 4 HOH A 11 311 20 HOH HOH . D 4 HOH A 12 312 15 HOH HOH . D 4 HOH A 13 313 10 HOH HOH . D 4 HOH A 14 314 21 HOH HOH . D 4 HOH A 15 315 4 HOH HOH . D 4 HOH A 16 316 19 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 P P1 POP . . . C 3 82.232 -44.244 106.542 0.8 89.46 ? P1 POP 202 A 1 HETATM 2 O O1 POP . . . C 3 83.15 -43.305 105.793 0.8 88.41 ? O1 POP 202 A 1 HETATM 3 O O2 POP . . . C 3 82.726 -44.649 107.908 0.8 88.93 ? O2 POP 202 A 1 HETATM 4 O O3 POP . . . C 3 80.784 -43.831 106.523 0.8 87.78 ? O3 POP 202 A 1 HETATM 5 O O POP . . . C 3 82.272 -45.61 105.673 0.8 91.63 ? O POP 202 A 1 HETATM 6 P P2 POP . . . C 3 81.596 -47.016 106.119 0.8 92.2 ? P2 POP 202 A 1 HETATM 7 O O4 POP . . . C 3 80.929 -47.511 104.856 0.8 92.27 ? O4 POP 202 A 1 HETATM 8 O O5 POP . . . C 3 82.764 -47.87 106.55 0.8 90.23 ? O5 POP 202 A 1 HETATM 9 O O6 POP . . . C 3 80.624 -46.69 107.23 0.8 91.57 ? O6 POP 202 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 9 #