data_3SK4 # _model_server_result.job_id '_OyoHdWPwm9U5m2JfMD0PQ' _model_server_result.datetime_utc '2024-10-11 10:22:46' _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 3sk4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":150}' # _entry.id 3SK4 # _exptl.entry_id 3SK4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 2 _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 94.38 _cell.angle_gamma 90 _cell.entry_id 3SK4 _cell.length_a 31.213 _cell.length_b 60.51 _cell.length_c 38.626 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SK4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 277 n n P2 O5P THP sing 278 n n P2 O6P THP sing 279 n n P2 O5' THP sing 280 n n O5P HOP5 THP sing 281 n n O6P HOP6 THP sing 282 n n P1 O1P THP doub 283 n n P1 O2P THP sing 284 n n P1 O3P THP sing 285 n n P1 O3' THP sing 286 n n O2P HOP2 THP sing 287 n n O3P HOP3 THP sing 288 n n O5' C5' THP sing 289 n n C5' C4' THP sing 290 n n C5' "H5'1" THP sing 291 n n C5' "H5'2" THP sing 292 n n C4' O4' THP sing 293 n n C4' C3' THP sing 294 n n C4' H4' THP sing 295 n n O4' C1' THP sing 296 n n C3' O3' THP sing 297 n n C3' C2' THP sing 298 n n C3' H3' THP sing 299 n n C2' C1' THP sing 300 n n C2' "H2'1" THP sing 301 n n C2' "H2'2" THP sing 302 n n C1' N1 THP sing 303 n n C1' H1' THP sing 304 n n N1 C2 THP sing 305 n n N1 C6 THP sing 306 n n C2 O2 THP doub 307 n n C2 N3 THP sing 308 n n N3 C4 THP sing 309 n n N3 H3 THP sing 310 n n C4 O4 THP doub 311 n n C4 C5 THP sing 312 n n C5 C5M THP sing 313 n n C5 C6 THP doub 314 n n C5M H51 THP sing 315 n n C5M H52 THP sing 316 n n C5M H53 THP sing 317 n n C6 H6 THP sing 318 n n # _atom_sites.entry_id 3SK4 _atom_sites.fract_transf_matrix[1][1] 0.032038 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002454 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016526 _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] 0.025965 _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 THP A 1 150 150 THP THP . C 3 HOH A 1 151 151 HOH HOH . C 3 HOH A 2 152 152 HOH HOH . C 3 HOH A 3 153 153 HOH HOH . C 3 HOH A 4 154 154 HOH HOH . C 3 HOH A 5 155 155 HOH HOH . C 3 HOH A 6 156 156 HOH HOH . C 3 HOH A 7 157 157 HOH HOH . C 3 HOH A 8 158 158 HOH HOH . C 3 HOH A 9 159 159 HOH HOH . C 3 HOH A 10 160 160 HOH HOH . C 3 HOH A 11 161 161 HOH HOH . C 3 HOH A 12 162 162 HOH HOH . C 3 HOH A 13 163 163 HOH HOH . C 3 HOH A 14 164 164 HOH HOH . C 3 HOH A 15 165 165 HOH HOH . C 3 HOH A 16 166 166 HOH HOH . C 3 HOH A 17 167 167 HOH HOH . C 3 HOH A 18 168 168 HOH HOH . C 3 HOH A 19 169 169 HOH HOH . C 3 HOH A 20 170 170 HOH HOH . C 3 HOH A 21 171 171 HOH HOH . C 3 HOH A 22 172 172 HOH HOH . C 3 HOH A 23 173 173 HOH HOH . C 3 HOH A 24 174 174 HOH HOH . C 3 HOH A 25 175 175 HOH HOH . C 3 HOH A 26 176 176 HOH HOH . C 3 HOH A 27 177 177 HOH HOH . C 3 HOH A 28 178 178 HOH HOH . C 3 HOH A 29 179 179 HOH HOH . C 3 HOH A 30 180 180 HOH HOH . C 3 HOH A 31 181 181 HOH HOH . C 3 HOH A 32 182 182 HOH HOH . C 3 HOH A 33 183 183 HOH HOH . C 3 HOH A 34 184 184 HOH HOH . C 3 HOH A 35 185 185 HOH HOH . C 3 HOH A 36 186 186 HOH HOH . C 3 HOH A 37 187 187 HOH HOH . C 3 HOH A 38 188 188 HOH HOH . C 3 HOH A 39 189 189 HOH HOH . C 3 HOH A 40 190 190 HOH HOH . C 3 HOH A 41 191 191 HOH HOH . C 3 HOH A 42 192 192 HOH HOH . C 3 HOH A 43 193 193 HOH HOH . C 3 HOH A 44 194 194 HOH HOH . C 3 HOH A 45 195 195 HOH HOH . C 3 HOH A 46 196 196 HOH HOH . C 3 HOH A 47 197 197 HOH HOH . C 3 HOH A 48 198 198 HOH HOH . C 3 HOH A 49 199 199 HOH HOH . C 3 HOH A 50 200 200 HOH HOH . C 3 HOH A 51 201 201 HOH HOH . C 3 HOH A 52 202 202 HOH HOH . C 3 HOH A 53 203 203 HOH HOH . C 3 HOH A 54 204 204 HOH HOH . C 3 HOH A 55 205 205 HOH HOH . C 3 HOH A 56 206 206 HOH HOH . C 3 HOH A 57 207 207 HOH HOH . C 3 HOH A 58 208 208 HOH HOH . C 3 HOH A 59 209 209 HOH HOH . C 3 HOH A 60 210 210 HOH HOH . C 3 HOH A 61 211 211 HOH HOH . C 3 HOH A 62 212 212 HOH HOH . C 3 HOH A 63 213 213 HOH HOH . C 3 HOH A 64 214 214 HOH HOH . C 3 HOH A 65 215 215 HOH HOH . C 3 HOH A 66 216 216 HOH HOH . C 3 HOH A 67 217 217 HOH HOH . C 3 HOH A 68 218 218 HOH HOH . C 3 HOH A 69 219 219 HOH HOH . C 3 HOH A 70 220 220 HOH HOH . C 3 HOH A 71 221 221 HOH HOH . C 3 HOH A 72 222 222 HOH HOH . C 3 HOH A 73 223 223 HOH HOH . C 3 HOH A 74 224 224 HOH HOH . C 3 HOH A 75 225 225 HOH HOH . C 3 HOH A 76 226 226 HOH HOH . C 3 HOH A 77 227 227 HOH HOH . C 3 HOH A 78 228 228 HOH HOH . C 3 HOH A 79 229 229 HOH HOH . C 3 HOH A 80 230 230 HOH HOH . C 3 HOH A 81 231 231 HOH HOH . C 3 HOH A 82 232 232 HOH HOH . C 3 HOH A 83 233 233 HOH HOH . C 3 HOH A 84 234 234 HOH HOH . C 3 HOH A 85 235 235 HOH HOH . C 3 HOH A 86 236 236 HOH HOH . C 3 HOH A 87 237 237 HOH HOH . C 3 HOH A 88 238 238 HOH HOH . C 3 HOH A 89 239 239 HOH HOH . C 3 HOH A 90 240 240 HOH HOH . C 3 HOH A 91 241 241 HOH HOH . C 3 HOH A 92 242 242 HOH HOH . C 3 HOH A 93 243 243 HOH HOH . C 3 HOH A 94 244 244 HOH HOH . C 3 HOH A 95 245 245 HOH HOH . C 3 HOH A 96 246 246 HOH HOH . C 3 HOH A 97 247 247 HOH HOH . C 3 HOH A 98 248 248 HOH HOH . C 3 HOH A 99 249 249 HOH HOH . C 3 HOH A 100 250 250 HOH HOH . C 3 HOH A 101 251 251 HOH HOH . C 3 HOH A 102 252 252 HOH HOH . C 3 HOH A 103 253 253 HOH HOH . C 3 HOH A 104 254 254 HOH HOH . C 3 HOH A 105 255 255 HOH HOH . C 3 HOH A 106 256 256 HOH HOH . C 3 HOH A 107 257 257 HOH HOH . C 3 HOH A 108 258 258 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 . . . B 2 18.086 -1.95 4.783 1 12.92 ? P2 THP 150 A 1 HETATM 2 O O4P THP . . . B 2 18.068 -3.374 5.134 1 12.7 ? O4P THP 150 A 1 HETATM 3 O O5P THP . . . B 2 16.773 -1.175 5.283 1 16.44 ? O5P THP 150 A 1 HETATM 4 O O6P THP . . . B 2 19.31 -1.231 5.511 1 15.21 ? O6P THP 150 A 1 HETATM 5 P P1 THP . . . B 2 21.316 1.558 1.064 1 16.52 ? P1 THP 150 A 1 HETATM 6 O O1P THP . . . B 2 22.287 2.144 0.123 1 15.75 ? O1P THP 150 A 1 HETATM 7 O O2P THP . . . B 2 21.995 0.364 1.922 1 18.61 ? O2P THP 150 A 1 HETATM 8 O O3P THP . . . B 2 20.597 2.556 2.076 1 15.93 ? O3P THP 150 A 1 HETATM 9 O O5' THP . . . B 2 18.116 -1.834 3.141 1 12.54 ? O5' THP 150 A 1 HETATM 10 C C5' THP . . . B 2 18.319 -0.508 2.707 1 14.71 ? C5' THP 150 A 1 HETATM 11 C C4' THP . . . B 2 19.094 -0.661 1.392 1 10.58 ? C4' THP 150 A 1 HETATM 12 O O4' THP . . . B 2 18.487 -1.735 0.693 1 11.02 ? O4' THP 150 A 1 HETATM 13 C C3' THP . . . B 2 18.937 0.612 0.504 1 12.89 ? C3' THP 150 A 1 HETATM 14 O O3' THP . . . B 2 20.217 0.98 -0.004 1 15.72 ? O3' THP 150 A 1 HETATM 15 C C2' THP . . . B 2 18.049 0.118 -0.674 1 9.37 ? C2' THP 150 A 1 HETATM 16 C C1' THP . . . B 2 18.329 -1.408 -0.722 1 6.46 ? C1' THP 150 A 1 HETATM 17 N N1 THP . . . B 2 17.02 -1.984 -1.096 1 8.91 ? N1 THP 150 A 1 HETATM 18 C C2 THP . . . B 2 16.741 -2.195 -2.414 1 13.77 ? C2 THP 150 A 1 HETATM 19 O O2 THP . . . B 2 17.601 -1.894 -3.232 1 13.72 ? O2 THP 150 A 1 HETATM 20 N N3 THP . . . B 2 15.586 -2.732 -2.838 1 13.93 ? N3 THP 150 A 1 HETATM 21 C C4 THP . . . B 2 14.631 -3 -1.931 1 13.01 ? C4 THP 150 A 1 HETATM 22 O O4 THP . . . B 2 13.545 -3.37 -2.386 1 11.89 ? O4 THP 150 A 1 HETATM 23 C C5 THP . . . B 2 14.876 -2.777 -0.537 1 10.62 ? C5 THP 150 A 1 HETATM 24 C C5M THP . . . B 2 13.844 -3.083 0.513 1 11.73 ? C5M THP 150 A 1 HETATM 25 C C6 THP . . . B 2 16.082 -2.274 -0.116 1 9.34 ? C6 THP 150 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 25 #