data_1OGK # _model_server_result.job_id c_rM1S2hkKx-7zQY_jUxiQ _model_server_result.datetime_utc '2024-11-15 03:12:47' _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 1ogk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1280}' # _entry.id 1OGK # _exptl.entry_id 1OGK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 388.162 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "DEOXYURIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 101.35 _cell.angle_gamma 90 _cell.entry_id 1OGK _cell.length_a 106.386 _cell.length_b 50.307 _cell.length_c 111.387 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1OGK _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E 1 1 C,D,F,G 2 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 ? 2 E N N ? 2 F N N ? 2 G N N # _chem_comp.formula 'C9 H14 N2 O11 P2' _chem_comp.formula_weight 388.162 _chem_comp.id DUD _chem_comp.mon_nstd_flag . _chem_comp.name "DEOXYURIDINE-5'-DIPHOSPHATE" _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 N1 C2 DUD sing 83 n n N1 C6 DUD sing 84 n n N1 C1' DUD sing 85 n n C2 N3 DUD sing 86 n n C2 O2 DUD doub 87 n n N3 C4 DUD sing 88 n n N3 HN3 DUD sing 89 n n C4 C5 DUD sing 90 n n C4 O4 DUD doub 91 n n C5 C6 DUD doub 92 n n C5 H5 DUD sing 93 n n C6 H6 DUD sing 94 n n C1' C2' DUD sing 95 n n C1' O4' DUD sing 96 n n C1' H1' DUD sing 97 n n C2' C3' DUD sing 98 n n C2' "H2'1" DUD sing 99 n n C2' "H2'2" DUD sing 100 n n C3' C4' DUD sing 101 n n C3' O3' DUD sing 102 n n C3' H3' DUD sing 103 n n C4' O4' DUD sing 104 n n C4' C5' DUD sing 105 n n C4' H4' DUD sing 106 n n O3' HO3' DUD sing 107 n n C5' O5' DUD sing 108 n n C5' "H5'1" DUD sing 109 n n C5' "H5'2" DUD sing 110 n n O5' PA DUD sing 111 n n PA O1A DUD doub 112 n n PA O2A DUD sing 113 n n PA O3A DUD sing 114 n n O2A HOA2 DUD sing 115 n n O3A PB DUD sing 116 n n PB O1B DUD doub 117 n n PB O2B DUD sing 118 n n PB O3B DUD sing 119 n n O2B HOB2 DUD sing 120 n n O3B HOB3 DUD sing 121 n n # _atom_sites.entry_id 1OGK _atom_sites.fract_transf_matrix[1][1] 0.0094 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001886 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019878 _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] 0.009157 _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 DUD B 1 1280 1280 DUD DUD . F 2 DUD D 1 1280 1280 DUD DUD . G 2 DUD E 1 1281 1281 DUD DUD . # 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 DUD . . . F 2 -6.971 5.518 101.09 1 62.87 ? N1 DUD 1280 D 1 HETATM 2 C C2 DUD . . . F 2 -7.757 5.77 102.175 1 63.42 ? C2 DUD 1280 D 1 HETATM 3 N N3 DUD . . . F 2 -7.486 5.216 103.379 1 64.37 ? N3 DUD 1280 D 1 HETATM 4 C C4 DUD . . . F 2 -6.422 4.369 103.544 1 64.02 ? C4 DUD 1280 D 1 HETATM 5 C C5 DUD . . . F 2 -5.598 4.083 102.448 1 63.55 ? C5 DUD 1280 D 1 HETATM 6 C C6 DUD . . . F 2 -5.898 4.684 101.203 1 63.24 ? C6 DUD 1280 D 1 HETATM 7 O O2 DUD . . . F 2 -8.74 6.523 102.066 1 63.61 ? O2 DUD 1280 D 1 HETATM 8 O O4 DUD . . . F 2 -6.178 3.86 104.666 1 61.48 ? O4 DUD 1280 D 1 HETATM 9 C C1' DUD . . . F 2 -7.327 6.178 99.832 1 62.44 ? C1' DUD 1280 D 1 HETATM 10 C C2' DUD . . . F 2 -6.97 7.672 99.822 1 62.25 ? C2' DUD 1280 D 1 HETATM 11 C C3' DUD . . . F 2 -6.797 8.048 98.353 1 61.66 ? C3' DUD 1280 D 1 HETATM 12 C C4' DUD . . . F 2 -6.377 6.716 97.726 1 62.05 ? C4' DUD 1280 D 1 HETATM 13 O O4' DUD . . . F 2 -6.617 5.684 98.71 1 63.18 ? O4' DUD 1280 D 1 HETATM 14 O O3' DUD . . . F 2 -8.021 8.57 97.819 1 61.02 ? O3' DUD 1280 D 1 HETATM 15 C C5' DUD . . . F 2 -4.913 6.643 97.337 1 61.96 ? C5' DUD 1280 D 1 HETATM 16 O O5' DUD . . . F 2 -4.701 5.323 96.822 1 61.2 ? O5' DUD 1280 D 1 HETATM 17 P PA DUD . . . F 2 -3.797 5.05 95.616 1 59.54 ? PA DUD 1280 D 1 HETATM 18 O O1A DUD . . . F 2 -2.507 5.931 95.776 1 57.98 ? O1A DUD 1280 D 1 HETATM 19 O O2A DUD . . . F 2 -3.553 3.538 95.642 1 56.28 ? O2A DUD 1280 D 1 HETATM 20 O O3A DUD . . . F 2 -4.592 5.427 94.325 1 61.03 ? O3A DUD 1280 D 1 HETATM 21 P PB DUD . . . F 2 -4.251 6.514 93.27 1 62.54 ? PB DUD 1280 D 1 HETATM 22 O O1B DUD . . . F 2 -3.287 5.822 92.314 1 60.65 ? O1B DUD 1280 D 1 HETATM 23 O O2B DUD . . . F 2 -3.676 7.843 93.805 1 59.79 ? O2B DUD 1280 D 1 HETATM 24 O O3B DUD . . . F 2 -5.543 6.758 92.503 1 60.67 ? O3B DUD 1280 D 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 24 #