data_3HP1 # _model_server_result.job_id 8SAi7_WINOURL-GKQIYOLw _model_server_result.datetime_utc '2025-03-04 07:24:56' _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 3hp1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 3HP1 # _exptl.entry_id 3HP1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 242.229 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description L-deoxythymidine _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 3HP1 _cell.length_a 79.78 _cell.length_b 79.78 _cell.length_c 93.7 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3HP1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_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 1,2 # 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 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 79.78 79.78 46.85 # _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 # _chem_comp.formula 'C10 H14 N2 O5' _chem_comp.formula_weight 242.229 _chem_comp.id LLT _chem_comp.mon_nstd_flag . _chem_comp.name L-deoxythymidine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "L-thymidine;beta-L-thymidine;L-dT;2'-deoxy-L-thymidine;1-(2-deoxy-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione" # 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 O4 C4 LLT doub 238 n n N3 C4 LLT sing 239 n n C4 C5 LLT sing 240 n n C5 C7 LLT sing 241 n n C5 C6 LLT doub 242 n n C7 H7 LLT sing 243 n n C7 H7A LLT sing 244 n n C7 H7B LLT sing 245 n n N1 C6 LLT sing 246 n n C6 H6 LLT sing 247 n n N3 C2 LLT sing 248 n n N3 HN3 LLT sing 249 n n O2 C2 LLT doub 250 n n C2 N1 LLT sing 251 n n N1 C1' LLT sing 252 n n O4' C1' LLT sing 253 n n C1' C2' LLT sing 254 n n C1' H1' LLT sing 255 n n O4' C4' LLT sing 256 n n C4' C5' LLT sing 257 n n C4' C3' LLT sing 258 n n C4' H4' LLT sing 259 n n O5' C5' LLT sing 260 n n C5' H5' LLT sing 261 n n C5' "H5'A" LLT sing 262 n n O5' HO5' LLT sing 263 n n C2' C3' LLT sing 264 n n O3' C3' LLT sing 265 n n C3' H3' LLT sing 266 n n O3' HO3' LLT sing 267 n n C2' H2' LLT sing 268 n n C2' "H2'A" LLT sing 269 n n # _atom_sites.entry_id 3HP1 _atom_sites.fract_transf_matrix[1][1] 0.012534 _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] 0.012534 _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] 0.010672 _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 ADP A 1 301 301 ADP ADP . C 3 LLT A 1 401 401 LLT LLT . D 4 HOH A 1 261 1 HOH HOH . D 4 HOH A 2 262 2 HOH HOH . D 4 HOH A 3 263 3 HOH HOH . D 4 HOH A 4 264 4 HOH HOH . D 4 HOH A 5 265 5 HOH HOH . D 4 HOH A 6 266 6 HOH HOH . D 4 HOH A 7 267 7 HOH HOH . D 4 HOH A 8 268 8 HOH HOH . D 4 HOH A 9 269 9 HOH HOH . D 4 HOH A 10 270 10 HOH HOH . D 4 HOH A 11 271 11 HOH HOH . D 4 HOH A 12 272 12 HOH HOH . D 4 HOH A 13 273 13 HOH HOH . D 4 HOH A 14 274 14 HOH HOH . D 4 HOH A 15 275 15 HOH HOH . D 4 HOH A 16 276 16 HOH HOH . D 4 HOH A 17 277 17 HOH HOH . D 4 HOH A 18 278 18 HOH HOH . D 4 HOH A 19 279 22 HOH HOH . D 4 HOH A 20 280 23 HOH HOH . D 4 HOH A 21 281 24 HOH HOH . D 4 HOH A 22 282 25 HOH HOH . D 4 HOH A 23 283 26 HOH HOH . D 4 HOH A 24 284 27 HOH HOH . D 4 HOH A 25 285 28 HOH HOH . D 4 HOH A 26 286 29 HOH HOH . D 4 HOH A 27 287 30 HOH HOH . D 4 HOH A 28 288 31 HOH HOH . D 4 HOH A 29 289 32 HOH HOH . D 4 HOH A 30 290 33 HOH HOH . D 4 HOH A 31 291 34 HOH HOH . D 4 HOH A 32 292 35 HOH HOH . D 4 HOH A 33 293 36 HOH HOH . D 4 HOH A 34 294 38 HOH HOH . D 4 HOH A 35 295 39 HOH HOH . D 4 HOH A 36 296 40 HOH HOH . D 4 HOH A 37 297 41 HOH HOH . D 4 HOH A 38 298 42 HOH HOH . D 4 HOH A 39 299 43 HOH HOH . D 4 HOH A 40 300 44 HOH HOH . D 4 HOH A 41 302 45 HOH HOH . D 4 HOH A 42 303 46 HOH HOH . D 4 HOH A 43 304 47 HOH HOH . D 4 HOH A 44 305 48 HOH HOH . D 4 HOH A 45 306 49 HOH HOH . D 4 HOH A 46 307 50 HOH HOH . D 4 HOH A 47 308 51 HOH HOH . D 4 HOH A 48 309 52 HOH HOH . D 4 HOH A 49 310 53 HOH HOH . D 4 HOH A 50 311 54 HOH HOH . D 4 HOH A 51 312 55 HOH HOH . D 4 HOH A 52 313 56 HOH HOH . D 4 HOH A 53 314 57 HOH HOH . D 4 HOH A 54 315 58 HOH HOH . D 4 HOH A 55 316 59 HOH HOH . D 4 HOH A 56 317 60 HOH HOH . D 4 HOH A 57 318 61 HOH HOH . D 4 HOH A 58 319 62 HOH HOH . D 4 HOH A 59 320 63 HOH HOH . D 4 HOH A 60 321 65 HOH HOH . D 4 HOH A 61 322 66 HOH HOH . D 4 HOH A 62 323 67 HOH HOH . D 4 HOH A 63 324 68 HOH HOH . D 4 HOH A 64 325 69 HOH HOH . D 4 HOH A 65 326 70 HOH HOH . D 4 HOH A 66 327 72 HOH HOH . D 4 HOH A 67 328 73 HOH HOH . D 4 HOH A 68 329 74 HOH HOH . D 4 HOH A 69 330 75 HOH HOH . D 4 HOH A 70 331 76 HOH HOH . D 4 HOH A 71 332 77 HOH HOH . D 4 HOH A 72 333 78 HOH HOH . D 4 HOH A 73 334 80 HOH HOH . D 4 HOH A 74 335 81 HOH HOH . D 4 HOH A 75 336 82 HOH HOH . D 4 HOH A 76 337 84 HOH HOH . D 4 HOH A 77 338 85 HOH HOH . D 4 HOH A 78 339 86 HOH HOH . D 4 HOH A 79 340 87 HOH HOH . D 4 HOH A 80 341 89 HOH HOH . D 4 HOH A 81 342 90 HOH HOH . D 4 HOH A 82 343 91 HOH HOH . D 4 HOH A 83 344 93 HOH HOH . D 4 HOH A 84 345 94 HOH HOH . D 4 HOH A 85 346 95 HOH HOH . D 4 HOH A 86 347 96 HOH HOH . D 4 HOH A 87 348 97 HOH HOH . D 4 HOH A 88 349 98 HOH HOH . D 4 HOH A 89 350 101 HOH HOH . D 4 HOH A 90 351 102 HOH HOH . D 4 HOH A 91 352 103 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 O4 LLT . . . C 3 62.721 33.04 17.468 1 31.75 ? O4 LLT 401 A 1 HETATM 2 C C4 LLT . . . C 3 64.018 33.245 17.818 1 30.99 ? C4 LLT 401 A 1 HETATM 3 C C5 LLT . . . C 3 64.422 34.504 18.209 1 32.08 ? C5 LLT 401 A 1 HETATM 4 C C7 LLT . . . C 3 63.451 35.646 18.251 1 32.98 ? C7 LLT 401 A 1 HETATM 5 C C6 LLT . . . C 3 65.747 34.696 18.574 1 32.61 ? C6 LLT 401 A 1 HETATM 6 N N3 LLT . . . C 3 64.906 32.23 17.79 1 29.44 ? N3 LLT 401 A 1 HETATM 7 C C2 LLT . . . C 3 66.194 32.463 18.123 1 32.09 ? C2 LLT 401 A 1 HETATM 8 O O2 LLT . . . C 3 67.061 31.422 18.085 1 33.45 ? O2 LLT 401 A 1 HETATM 9 N N1 LLT . . . C 3 66.615 33.673 18.518 1 31.28 ? N1 LLT 401 A 1 HETATM 10 C C1' LLT . . . C 3 67.995 33.92 18.912 1 33.46 ? C1' LLT 401 A 1 HETATM 11 O O4' LLT . . . C 3 68.307 35.327 18.883 1 36.43 ? O4' LLT 401 A 1 HETATM 12 C C4' LLT . . . C 3 69.251 35.673 19.901 1 36.02 ? C4' LLT 401 A 1 HETATM 13 C C5' LLT . . . C 3 68.779 36.917 20.64 1 38.07 ? C5' LLT 401 A 1 HETATM 14 O O5' LLT . . . C 3 69.221 38.106 19.941 1 39.33 ? O5' LLT 401 A 1 HETATM 15 C C3' LLT . . . C 3 69.353 34.464 20.816 1 37.17 ? C3' LLT 401 A 1 HETATM 16 O O3' LLT . . . C 3 70.629 33.857 20.568 1 37.54 ? O3' LLT 401 A 1 HETATM 17 C C2' LLT . . . C 3 68.23 33.53 20.374 1 35.73 ? C2' LLT 401 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 17 #