data_1NUC # _model_server_result.job_id tRC_SF4U8NrxDCLoqW2S2A _model_server_result.datetime_utc '2025-02-19 22:37:09' _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 1nuc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":151}' # _entry.id 1NUC # _exptl.entry_id 1NUC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-3',5'-DIPHOSPHATE" _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 90 _cell.entry_id 1NUC _cell.length_a 47.4 _cell.length_b 47.4 _cell.length_c 62.8 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NUC _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # _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 # _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 # 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 OD2 ASP 21 A ASP 21 1_555 B CA CA . A CA 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 B CA CA . A CA 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 B CA CA . A CA 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.776 ? metalc ? metalc4 B CA CA . A CA 150 1_555 C O4P THP . A THP 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.691 ? metalc ? metalc5 B CA CA . A CA 150 1_555 D O HOH . A HOH 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc6 B CA CA . A CA 150 1_555 D O HOH . A HOH 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc7 B CA CA . A CA 150 1_555 D O HOH . A HOH 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.544 ? # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id THP _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-3',5'-DIPHOSPHATE" _chem_comp.type 'dna linking' _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 P2 O4P THP doub 290 n n P2 O5P THP sing 291 n n P2 O6P THP sing 292 n n P2 O5' THP sing 293 n n O5P HOP5 THP sing 294 n n O6P HOP6 THP sing 295 n n P1 O1P THP doub 296 n n P1 O2P THP sing 297 n n P1 O3P THP sing 298 n n P1 O3' THP sing 299 n n O2P HOP2 THP sing 300 n n O3P HOP3 THP sing 301 n n O5' C5' THP sing 302 n n C5' C4' THP sing 303 n n C5' "H5'1" THP sing 304 n n C5' "H5'2" THP sing 305 n n C4' O4' THP sing 306 n n C4' C3' THP sing 307 n n C4' H4' THP sing 308 n n O4' C1' THP sing 309 n n C3' O3' THP sing 310 n n C3' C2' THP sing 311 n n C3' H3' THP sing 312 n n C2' C1' THP sing 313 n n C2' "H2'1" THP sing 314 n n C2' "H2'2" THP sing 315 n n C1' N1 THP sing 316 n n C1' H1' THP sing 317 n n N1 C2 THP sing 318 n n N1 C6 THP sing 319 n n C2 O2 THP doub 320 n n C2 N3 THP sing 321 n n N3 C4 THP sing 322 n n N3 H3 THP sing 323 n n C4 O4 THP doub 324 n n C4 C5 THP sing 325 n n C5 C5M THP sing 326 n n C5 C6 THP doub 327 n n C5M H51 THP sing 328 n n C5M H52 THP sing 329 n n C5M H53 THP sing 330 n n C6 H6 THP sing 331 n n # _atom_sites.entry_id 1NUC _atom_sites.fract_transf_matrix[1][1] 0.021097 _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] 0.021097 _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] 0.015924 _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 CA A 1 150 142 CA CA . C 3 THP A 1 151 143 THP THP . D 4 HOH A 1 201 201 HOH HOH . D 4 HOH A 2 202 202 HOH HOH . D 4 HOH A 3 204 204 HOH HOH . D 4 HOH A 4 206 206 HOH HOH . D 4 HOH A 5 208 208 HOH HOH . D 4 HOH A 6 209 209 HOH HOH . D 4 HOH A 7 211 211 HOH HOH . D 4 HOH A 8 213 213 HOH HOH . D 4 HOH A 9 215 215 HOH HOH . D 4 HOH A 10 216 216 HOH HOH . D 4 HOH A 11 217 217 HOH HOH . D 4 HOH A 12 218 218 HOH HOH . D 4 HOH A 13 221 221 HOH HOH . D 4 HOH A 14 222 222 HOH HOH . D 4 HOH A 15 223 223 HOH HOH . D 4 HOH A 16 224 224 HOH HOH . D 4 HOH A 17 226 226 HOH HOH . D 4 HOH A 18 227 227 HOH HOH . D 4 HOH A 19 228 228 HOH HOH . D 4 HOH A 20 229 229 HOH HOH . D 4 HOH A 21 230 230 HOH HOH . D 4 HOH A 22 231 231 HOH HOH . D 4 HOH A 23 232 232 HOH HOH . D 4 HOH A 24 233 233 HOH HOH . D 4 HOH A 25 236 236 HOH HOH . D 4 HOH A 26 237 237 HOH HOH . D 4 HOH A 27 240 240 HOH HOH . D 4 HOH A 28 241 241 HOH HOH . D 4 HOH A 29 242 242 HOH HOH . D 4 HOH A 30 243 243 HOH HOH . D 4 HOH A 31 244 244 HOH HOH . D 4 HOH A 32 245 245 HOH HOH . D 4 HOH A 33 246 246 HOH HOH . D 4 HOH A 34 248 248 HOH HOH . D 4 HOH A 35 250 250 HOH HOH . D 4 HOH A 36 251 251 HOH HOH . D 4 HOH A 37 254 254 HOH HOH . D 4 HOH A 38 256 256 HOH HOH . D 4 HOH A 39 257 257 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 P2 THP . . . C 3 6.126 13.455 20.522 1 31.18 ? P2 THP 151 A 1 HETATM 2 O O4P THP . . . C 3 5.15 13.438 19.409 1 33.81 ? O4P THP 151 A 1 HETATM 3 O O5P THP . . . C 3 7.254 14.348 20.212 1 29.15 ? O5P THP 151 A 1 HETATM 4 O O6P THP . . . C 3 6.456 12.099 20.962 1 31.58 ? O6P THP 151 A 1 HETATM 5 P P1 THP . . . C 3 4.733 11.237 26.359 1 38.98 ? P1 THP 151 A 1 HETATM 6 O O1P THP . . . C 3 5.006 10.954 27.772 1 44.34 ? O1P THP 151 A 1 HETATM 7 O O2P THP . . . C 3 5.936 11.307 25.555 1 42.24 ? O2P THP 151 A 1 HETATM 8 O O3P THP . . . C 3 3.675 10.449 25.725 1 44.17 ? O3P THP 151 A 1 HETATM 9 O O5' THP . . . C 3 5.458 14.192 21.752 1 30.83 ? O5' THP 151 A 1 HETATM 10 C C5' THP . . . C 3 4.406 13.694 22.582 1 33.3 ? C5' THP 151 A 1 HETATM 11 C C4' THP . . . C 3 4.825 13.697 24.079 1 31.33 ? C4' THP 151 A 1 HETATM 12 O O4' THP . . . C 3 5.095 15.044 24.397 1 30.39 ? O4' THP 151 A 1 HETATM 13 C C3' THP . . . C 3 3.685 13.318 25.069 1 33.62 ? C3' THP 151 A 1 HETATM 14 O O3' THP . . . C 3 4.111 12.729 26.345 1 36.85 ? O3' THP 151 A 1 HETATM 15 C C2' THP . . . C 3 2.913 14.596 25.269 1 28.87 ? C2' THP 151 A 1 HETATM 16 C C1' THP . . . C 3 4.045 15.561 25.249 1 28.57 ? C1' THP 151 A 1 HETATM 17 N N1 THP . . . C 3 3.596 16.886 24.815 1 29.66 ? N1 THP 151 A 1 HETATM 18 C C2 THP . . . C 3 3.28 17.705 25.818 1 30.61 ? C2 THP 151 A 1 HETATM 19 O O2 THP . . . C 3 3.447 17.442 26.996 1 33.41 ? O2 THP 151 A 1 HETATM 20 N N3 THP . . . C 3 2.769 18.885 25.48 1 30.71 ? N3 THP 151 A 1 HETATM 21 C C4 THP . . . C 3 2.586 19.382 24.231 1 31.29 ? C4 THP 151 A 1 HETATM 22 O O4 THP . . . C 3 2.086 20.508 24.138 1 31.25 ? O4 THP 151 A 1 HETATM 23 C C5 THP . . . C 3 2.959 18.474 23.171 1 31.76 ? C5 THP 151 A 1 HETATM 24 C C5M THP . . . C 3 2.684 18.886 21.685 1 28.28 ? C5M THP 151 A 1 HETATM 25 C C6 THP . . . C 3 3.474 17.274 23.502 1 30.35 ? C6 THP 151 A 1 HETATM 26 H H3 THP . . . C 3 2.492 19.499 26.232 1 0 ? H3 THP 151 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 26 #