data_2W0S # _model_server_result.job_id iYttekLXBEkI3PRyXaluEA _model_server_result.datetime_utc '2024-11-13 12:26:45' _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 2w0s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1207}' # _entry.id 2W0S # _exptl.entry_id 2W0S _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 3 _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 90 _cell.entry_id 2W0S _cell.length_a 58.37 _cell.length_b 78.35 _cell.length_c 95.04 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2W0S _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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,C,D,E,F,L 1 1 B,G,H,I,J,K,M 1 2 A,C,D,E,F,L 2 2 B,G,H,I,J,K,M 2 3 # 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 'crystal symmetry operation' 2_454 -x-1/2,-y,z-1/2 -1 0 0 0 -1 0 0 0 1 -29.185 0 -47.52 2 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 2_455 -x-1/2,-y,z+1/2 -1 0 0 0 -1 0 0 0 1 -29.185 0 47.52 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 I N N ? 3 K 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 metalc ? metalc1 A OD1 ASP 13 A ASP 13 1_555 D MG MG . A MG 1206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc2 A OE2 GLU 145 A GLU 145 1_555 D MG MG . A MG 1206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? metalc ? metalc3 B OD1 ASP 13 B ASP 13 1_555 H MG MG . B MG 1206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc4 B OD2 ASP 92 B ASP 92 1_555 G MG MG . B MG 1205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc5 B OE2 GLU 145 B GLU 145 1_555 H MG MG . B MG 1206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? metalc ? metalc6 H MG MG . B MG 1206 1_555 I O3P BVP . B BVP 1207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? # _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 70 n n O3' H3' BVP sing 71 n n C3' C2' BVP sing 72 n n C3' C4' BVP sing 73 n n C3' H1 BVP sing 74 n n C2' C1' BVP sing 75 n n C2' "H2'1" BVP sing 76 n n C2' "H2'2" BVP sing 77 n n C1' O4' BVP sing 78 n n C1' N1 BVP sing 79 n n C1' H1' BVP sing 80 n n O4' C4' BVP sing 81 n n C4' C5' BVP sing 82 n n C4' H4' BVP sing 83 n n C5' O5' BVP sing 84 n n C5' "H5'1" BVP sing 85 n n C5' "H5'2" BVP sing 86 n n O5' P BVP sing 87 n n P O1P BVP doub 88 n n P O2P BVP sing 89 n n P O3P BVP sing 90 n n O2P H2P BVP sing 91 n n O3P H3P BVP sing 92 n n N1 C6 BVP sing 93 n n N1 C2 BVP sing 94 n n C6 C5 BVP doub 95 n n C6 H6 BVP sing 96 n n C5 C5A BVP sing 97 n n C5 C4 BVP sing 98 n n C5A C5B BVP doub 99 e n C5A H5A BVP sing 100 n n C5B BR BVP sing 101 n n C5B H5B BVP sing 102 n n C4 O4 BVP doub 103 n n C4 N3 BVP sing 104 n n N3 C2 BVP sing 105 n n N3 HN3 BVP sing 106 n n C2 O2 BVP doub 107 n n # _atom_sites.entry_id 2W0S _atom_sites.fract_transf_matrix[1][1] 0.017132 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012763 _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] 0.010522 _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 MG A 1 1205 1205 MG MG . D 2 MG A 1 1206 1206 MG MG . E 3 BVP A 1 1207 1207 BVP BVP . F 4 SO4 A 1 1208 1208 SO4 SO4 . G 2 MG B 1 1205 1205 MG MG . H 2 MG B 1 1206 1206 MG MG . I 3 BVP B 1 1207 1207 BVP BVP . J 4 SO4 B 1 1208 1208 SO4 SO4 . K 3 BVP B 1 1209 1209 BVP BVP . L 5 HOH A 1 2001 2001 HOH HOH . L 5 HOH A 2 2002 2002 HOH HOH . L 5 HOH A 3 2003 2003 HOH HOH . L 5 HOH A 4 2004 2004 HOH HOH . M 5 HOH B 1 2001 2001 HOH HOH . M 5 HOH B 2 2002 2002 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 . . . I 3 -12.366 -18.355 -27.598 1 44.51 ? O3' BVP 1207 B 1 HETATM 2 C C3' BVP . . . I 3 -12.215 -17.222 -26.797 1 30.57 ? C3' BVP 1207 B 1 HETATM 3 C C2' BVP . . . I 3 -10.712 -16.964 -26.536 1 43.02 ? C2' BVP 1207 B 1 HETATM 4 C C1' BVP . . . I 3 -10.372 -16.012 -27.688 1 42.35 ? C1' BVP 1207 B 1 HETATM 5 O O4' BVP . . . I 3 -11.513 -15.067 -27.703 1 36.26 ? O4' BVP 1207 B 1 HETATM 6 C C4' BVP . . . I 3 -12.672 -15.977 -27.626 1 32.15 ? C4' BVP 1207 B 1 HETATM 7 C C5' BVP . . . I 3 -13.977 -15.284 -27.153 1 31.66 ? C5' BVP 1207 B 1 HETATM 8 O O5' BVP . . . I 3 -13.704 -14.352 -26.087 1 49 ? O5' BVP 1207 B 1 HETATM 9 P P BVP . . . I 3 -14.462 -14.296 -24.612 1 40.1 ? P BVP 1207 B 1 HETATM 10 O O1P BVP . . . I 3 -13.305 -13.817 -23.527 1 25.58 ? O1P BVP 1207 B 1 HETATM 11 O O2P BVP . . . I 3 -15.568 -13.101 -24.668 1 18.93 ? O2P BVP 1207 B 1 HETATM 12 O O3P BVP . . . I 3 -15.069 -15.586 -24.212 1 51.55 ? O3P BVP 1207 B 1 HETATM 13 N N1 BVP . . . I 3 -8.943 -15.454 -27.808 1 37.86 ? N1 BVP 1207 B 1 HETATM 14 C C6 BVP . . . I 3 -8.112 -15.841 -28.872 1 29.62 ? C6 BVP 1207 B 1 HETATM 15 C C5 BVP . . . I 3 -6.816 -15.323 -28.945 1 32.98 ? C5 BVP 1207 B 1 HETATM 16 C C5A BVP . . . I 3 -5.96 -15.641 -29.998 1 34.04 ? C5A BVP 1207 B 1 HETATM 17 C C5B BVP . . . I 3 -6.558 -16.554 -31.061 1 37.5 ? C5B BVP 1207 B 1 HETATM 18 BR BR BVP . . . I 3 -5.398 -16.961 -32.443 0.43 32.49 ? BR BVP 1207 B 1 HETATM 19 C C4 BVP . . . I 3 -6.358 -14.417 -28.001 1 36.58 ? C4 BVP 1207 B 1 HETATM 20 O O4 BVP . . . I 3 -5.227 -13.937 -28.073 1 43.19 ? O4 BVP 1207 B 1 HETATM 21 N N3 BVP . . . I 3 -7.173 -14.042 -26.963 1 28.04 ? N3 BVP 1207 B 1 HETATM 22 C C2 BVP . . . I 3 -8.449 -14.567 -26.887 1 36.33 ? C2 BVP 1207 B 1 HETATM 23 O O2 BVP . . . I 3 -9.1 -14.161 -25.924 1 40.04 ? O2 BVP 1207 B 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 235 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 23 #