data_1OSN # _model_server_result.job_id nEJozS3LDLlMxw0fohTkmA _model_server_result.datetime_utc '2025-02-17 16:53:30' _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 1osn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1500}' # _entry.id 1OSN # _exptl.entry_id 1OSN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 413.115 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "(E)-5-(2-BROMOVINYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _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 94.8 _cell.angle_gamma 90 _cell.entry_id 1OSN _cell.length_a 99.7 _cell.length_b 54.2 _cell.length_c 167.8 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1OSN _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 PISA tetrameric 4 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,M 1 1 C,D,I,J,K,L 2 1 A,B,C,D,E,F,G,H,I,J,K,L,M 3 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 F N N ? 3 H N N ? 3 J N N ? 3 L N N # _chem_comp.formula 'C11 H14 Br N2 O8 P' _chem_comp.formula_weight 413.115 _chem_comp.id BVP _chem_comp.mon_nstd_flag n _chem_comp.name "(E)-5-(2-BROMOVINYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _chem_comp.type 'dna linking' _chem_comp.pdbx_synonyms BVDU-MP # 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 O3' C3' BVP sing 114 n n O3' H3' BVP sing 115 n n C3' C2' BVP sing 116 n n C3' C4' BVP sing 117 n n C3' H1 BVP sing 118 n n C2' C1' BVP sing 119 n n C2' "H2'1" BVP sing 120 n n C2' "H2'2" BVP sing 121 n n C1' O4' BVP sing 122 n n C1' N1 BVP sing 123 n n C1' H1' BVP sing 124 n n O4' C4' BVP sing 125 n n C4' C5' BVP sing 126 n n C4' H4' BVP sing 127 n n C5' O5' BVP sing 128 n n C5' "H5'1" BVP sing 129 n n C5' "H5'2" BVP sing 130 n n O5' P BVP sing 131 n n P O1P BVP doub 132 n n P O2P BVP sing 133 n n P O3P BVP sing 134 n n O2P H2P BVP sing 135 n n O3P H3P BVP sing 136 n n N1 C6 BVP sing 137 n n N1 C2 BVP sing 138 n n C6 C5 BVP doub 139 n n C6 H6 BVP sing 140 n n C5 C5A BVP sing 141 n n C5 C4 BVP sing 142 n n C5A C5B BVP doub 143 e n C5A H5A BVP sing 144 n n C5B BR BVP sing 145 n n C5B H5B BVP sing 146 n n C4 O4 BVP doub 147 n n C4 N3 BVP sing 148 n n N3 C2 BVP sing 149 n n N3 HN3 BVP sing 150 n n C2 O2 BVP doub 151 n n # _atom_sites.entry_id 1OSN _atom_sites.fract_transf_matrix[1][1] 0.01003 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000842 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01845 _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] 0.00598 _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 ADP A 1 400 400 ADP ADP . F 3 BVP A 1 500 500 BVP BDP . G 2 ADP B 1 1400 400 ADP ADP . H 3 BVP B 1 1500 500 BVP BDP . I 2 ADP C 1 2400 400 ADP ADP . J 3 BVP C 1 2500 500 BVP BDP . K 2 ADP D 1 3400 400 ADP ADP . L 3 BVP D 1 3500 500 BVP BDP . M 4 HOH A 1 600 600 HOH HOH . M 4 HOH A 2 601 601 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 O O3' BVP . . . H 3 51.241 34.771 60.499 1 34.04 ? O3' BVP 1500 B 1 HETATM 2 C C3' BVP . . . H 3 51.251 33.94 61.655 1 27.78 ? C3' BVP 1500 B 1 HETATM 3 C C2' BVP . . . H 3 51.798 32.546 61.395 1 24.46 ? C2' BVP 1500 B 1 HETATM 4 C C1' BVP . . . H 3 53.301 32.807 61.415 1 26.46 ? C1' BVP 1500 B 1 HETATM 5 O O4' BVP . . . H 3 53.507 33.949 62.274 1 28.98 ? O4' BVP 1500 B 1 HETATM 6 C C4' BVP . . . H 3 52.227 34.542 62.619 1 26.62 ? C4' BVP 1500 B 1 HETATM 7 C C5' BVP . . . H 3 51.949 34.256 64.114 1 36.7 ? C5' BVP 1500 B 1 HETATM 8 O O5' BVP . . . H 3 50.614 34.685 64.504 1 44.26 ? O5' BVP 1500 B 1 HETATM 9 P P BVP . . . H 3 49.502 33.689 65.185 1 40.02 ? P BVP 1500 B 1 HETATM 10 O O1P BVP . . . H 3 49.926 32.285 64.964 1 42.2 ? O1P BVP 1500 B 1 HETATM 11 O O2P BVP . . . H 3 48.188 33.915 64.538 1 50.99 ? O2P BVP 1500 B 1 HETATM 12 O O3P BVP . . . H 3 49.386 33.959 66.617 1 39.83 ? O3P BVP 1500 B 1 HETATM 13 N N1 BVP . . . H 3 54.197 31.669 61.91 1 26.69 ? N1 BVP 1500 B 1 HETATM 14 C C6 BVP . . . H 3 54.165 31.247 63.244 1 30.59 ? C6 BVP 1500 B 1 HETATM 15 C C5 BVP . . . H 3 55.02 30.163 63.696 1 35.26 ? C5 BVP 1500 B 1 HETATM 16 C C5A BVP . . . H 3 55.143 29.666 64.719 1 39.19 ? C5A BVP 1500 B 1 HETATM 17 C C5B BVP . . . H 3 55.864 30.122 65.801 1 54.37 ? C5B BVP 1500 B 1 HETATM 18 BR BR BVP . . . H 3 56.354 28.99 67.321 1 74.72 ? BR BVP 1500 B 1 HETATM 19 C C4 BVP . . . H 3 55.901 29.549 62.692 1 37.72 ? C4 BVP 1500 B 1 HETATM 20 O O4 BVP . . . H 3 56.694 28.602 62.928 1 53.69 ? O4 BVP 1500 B 1 HETATM 21 N N3 BVP . . . H 3 55.855 30.039 61.397 1 30.8 ? N3 BVP 1500 B 1 HETATM 22 C C2 BVP . . . H 3 55.044 31.06 60.987 1 32.9 ? C2 BVP 1500 B 1 HETATM 23 O O2 BVP . . . H 3 55.089 31.405 59.811 1 41.44 ? O2 BVP 1500 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 23 #