data_5NUC # _model_server_result.job_id gILcPZ_qjdKjAIlXIBN4kA _model_server_result.datetime_utc '2024-11-22 17:04:07' _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 5nuc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":151}' # _entry.id 5NUC # _exptl.entry_id 5NUC _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 5NUC _cell.length_a 47.8 _cell.length_b 47.8 _cell.length_c 62.6 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NUC _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 covale ? covale1 A C THR 22 A THR 22 1_555 A N PEC 23 A PEC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A C PEC 23 A PEC 23 1_555 A N LYS 24 A LYS 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? metalc ? metalc1 A OD2 ASP 21 A ASP 21 1_555 B CA CA . A CA 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 B CA CA . A CA 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 B CA CA . A CA 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.741 ? metalc ? metalc4 B CA CA . A CA 150 1_555 C O4P THP . A THP 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc5 B CA CA . A CA 150 1_555 D O HOH . A HOH 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc6 B CA CA . A CA 150 1_555 D O HOH . A HOH 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? # _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 ? # _atom_sites.entry_id 5NUC _atom_sites.fract_transf_matrix[1][1] 0.020921 _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] 0.020921 _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] 0.015974 _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 3 203 203 HOH HOH . D 4 HOH A 4 204 204 HOH HOH . D 4 HOH A 5 205 205 HOH HOH . D 4 HOH A 6 206 206 HOH HOH . D 4 HOH A 7 207 207 HOH HOH . D 4 HOH A 8 210 210 HOH HOH . D 4 HOH A 9 211 211 HOH HOH . D 4 HOH A 10 214 214 HOH HOH . D 4 HOH A 11 215 215 HOH HOH . D 4 HOH A 12 216 216 HOH HOH . D 4 HOH A 13 219 219 HOH HOH . D 4 HOH A 14 220 220 HOH HOH . D 4 HOH A 15 221 221 HOH HOH . D 4 HOH A 16 222 222 HOH HOH . D 4 HOH A 17 223 223 HOH HOH . D 4 HOH A 18 224 224 HOH HOH . D 4 HOH A 19 225 225 HOH HOH . D 4 HOH A 20 229 229 HOH HOH . D 4 HOH A 21 230 230 HOH HOH . D 4 HOH A 22 232 232 HOH HOH . D 4 HOH A 23 233 233 HOH HOH . D 4 HOH A 24 235 235 HOH HOH . D 4 HOH A 25 238 238 HOH HOH . D 4 HOH A 26 240 240 HOH HOH . D 4 HOH A 27 241 241 HOH HOH . D 4 HOH A 28 242 242 HOH HOH . D 4 HOH A 29 243 243 HOH HOH . D 4 HOH A 30 244 244 HOH HOH . D 4 HOH A 31 247 247 HOH HOH . D 4 HOH A 32 249 249 HOH HOH . D 4 HOH A 33 251 251 HOH HOH . D 4 HOH A 34 252 252 HOH HOH . D 4 HOH A 35 253 253 HOH HOH . D 4 HOH A 36 260 260 HOH HOH . D 4 HOH A 37 263 263 HOH HOH . D 4 HOH A 38 300 300 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 6.173 13.667 20.327 1 24.46 ? P2 THP 151 A 1 HETATM 2 O O4P THP . . . C 3 5.171 13.685 19.217 1 28.56 ? O4P THP 151 A 1 HETATM 3 O O5P THP . . . C 3 7.372 14.464 20.006 1 25.29 ? O5P THP 151 A 1 HETATM 4 O O6P THP . . . C 3 6.405 12.304 20.796 1 29.73 ? O6P THP 151 A 1 HETATM 5 P P1 THP . . . C 3 4.778 11.447 26.124 1 29.57 ? P1 THP 151 A 1 HETATM 6 O O1P THP . . . C 3 4.905 11.268 27.566 1 33.81 ? O1P THP 151 A 1 HETATM 7 O O2P THP . . . C 3 6.039 11.303 25.398 1 28.16 ? O2P THP 151 A 1 HETATM 8 O O3P THP . . . C 3 3.632 10.802 25.489 1 34.47 ? O3P THP 151 A 1 HETATM 9 O O5' THP . . . C 3 5.554 14.436 21.572 1 25.86 ? O5' THP 151 A 1 HETATM 10 C C5' THP . . . C 3 4.471 13.894 22.361 1 29.65 ? C5' THP 151 A 1 HETATM 11 C C4' THP . . . C 3 4.823 13.929 23.873 1 31.49 ? C4' THP 151 A 1 HETATM 12 O O4' THP . . . C 3 5.109 15.274 24.286 1 31.32 ? O4' THP 151 A 1 HETATM 13 C C3' THP . . . C 3 3.72 13.524 24.886 1 31.08 ? C3' THP 151 A 1 HETATM 14 O O3' THP . . . C 3 4.35 12.997 26.081 1 31.31 ? O3' THP 151 A 1 HETATM 15 C C2' THP . . . C 3 3 14.824 25.214 1 27.34 ? C2' THP 151 A 1 HETATM 16 C C1' THP . . . C 3 4.107 15.798 25.191 1 26.51 ? C1' THP 151 A 1 HETATM 17 N N1 THP . . . C 3 3.658 17.154 24.755 1 26.02 ? N1 THP 151 A 1 HETATM 18 C C2 THP . . . C 3 3.409 18 25.775 1 24.79 ? C2 THP 151 A 1 HETATM 19 O O2 THP . . . C 3 3.711 17.745 26.932 1 30 ? O2 THP 151 A 1 HETATM 20 N N3 THP . . . C 3 2.915 19.207 25.425 1 23.91 ? N3 THP 151 A 1 HETATM 21 C C4 THP . . . C 3 2.742 19.665 24.135 1 25.81 ? C4 THP 151 A 1 HETATM 22 O O4 THP . . . C 3 2.224 20.766 23.96 1 25.38 ? O4 THP 151 A 1 HETATM 23 C C5 THP . . . C 3 3.174 18.767 23.077 1 24.22 ? C5 THP 151 A 1 HETATM 24 C C5M THP . . . C 3 2.907 19.189 21.601 1 18.32 ? C5M THP 151 A 1 HETATM 25 C C6 THP . . . C 3 3.693 17.593 23.435 1 23.06 ? C6 THP 151 A 1 HETATM 26 H H3 THP . . . C 3 2.728 19.87 26.161 1 0 ? H3 THP 151 A 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 26 #