data_1OGK # _model_server_result.job_id DobOHwO3bH8T5GgilZW_ZA _model_server_result.datetime_utc '2024-11-15 03:20:06' _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":"E","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 . . . E 2 6.858 4.792 54.235 1 62.15 ? N1 DUD 1280 B 1 HETATM 2 C C2 DUD . . . E 2 5.568 4.994 53.893 1 63.01 ? C2 DUD 1280 B 1 HETATM 3 N N3 DUD . . . E 2 5.123 6.105 53.322 1 63.74 ? N3 DUD 1280 B 1 HETATM 4 C C4 DUD . . . E 2 5.955 7.098 53.05 1 63.53 ? C4 DUD 1280 B 1 HETATM 5 C C5 DUD . . . E 2 7.298 6.931 53.381 1 63.52 ? C5 DUD 1280 B 1 HETATM 6 C C6 DUD . . . E 2 7.733 5.756 54.001 1 62.66 ? C6 DUD 1280 B 1 HETATM 7 O O2 DUD . . . E 2 4.721 4.117 54.075 1 63.5 ? O2 DUD 1280 B 1 HETATM 8 O O4 DUD . . . E 2 5.521 8.128 52.51 1 60.55 ? O4 DUD 1280 B 1 HETATM 9 C C1' DUD . . . E 2 7.225 3.53 54.885 1 61.98 ? C1' DUD 1280 B 1 HETATM 10 C C2' DUD . . . E 2 7.317 2.363 53.963 1 61.71 ? C2' DUD 1280 B 1 HETATM 11 C C3' DUD . . . E 2 8.271 1.421 54.629 1 61.17 ? C3' DUD 1280 B 1 HETATM 12 C C4' DUD . . . E 2 9.141 2.3 55.476 1 61.53 ? C4' DUD 1280 B 1 HETATM 13 O O4' DUD . . . E 2 8.49 3.525 55.463 1 62.45 ? O4' DUD 1280 B 1 HETATM 14 O O3' DUD . . . E 2 7.556 0.53 55.443 1 60.49 ? O3' DUD 1280 B 1 HETATM 15 C C5' DUD . . . E 2 10.545 2.528 54.945 1 61.64 ? C5' DUD 1280 B 1 HETATM 16 O O5' DUD . . . E 2 11.239 3.383 55.844 1 60.13 ? O5' DUD 1280 B 1 HETATM 17 P PA DUD . . . E 2 12.66 3.199 56.222 1 56.35 ? PA DUD 1280 B 1 HETATM 18 O O1A DUD . . . E 2 13.398 2.912 54.943 1 57.2 ? O1A DUD 1280 B 1 HETATM 19 O O2A DUD . . . E 2 13.03 4.493 56.87 1 55.05 ? O2A DUD 1280 B 1 HETATM 20 O O3A DUD . . . E 2 12.813 2.053 57.244 1 59.82 ? O3A DUD 1280 B 1 HETATM 21 P PB DUD . . . E 2 13.571 0.698 57.287 1 60.94 ? PB DUD 1280 B 1 HETATM 22 O O1B DUD . . . E 2 15.014 0.882 57.663 1 60.5 ? O1B DUD 1280 B 1 HETATM 23 O O2B DUD . . . E 2 13.607 -0.111 56.014 1 59.67 ? O2B DUD 1280 B 1 HETATM 24 O O3B DUD . . . E 2 13.017 -0.178 58.354 1 60.13 ? O3B DUD 1280 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 24 #