data_3KFX # _model_server_result.job_id 3CDjWv6phbgcKdFXTHM0hg _model_server_result.datetime_utc '2025-03-04 07:46:15' _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 3kfx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 3KFX # _exptl.entry_id 3KFX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 241.244 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5-METHYL-2'-DEOXYCYTIDINE" _entity.pdbx_number_of_molecules 2 _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 3KFX _cell.length_a 52.74 _cell.length_b 132.95 _cell.length_c 156.89 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KFX _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 tetrameric 4 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,B,C,D,E,F,G,H 1 1 A,B,C,D,E,F,G,H 2 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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N N # _chem_comp.formula 'C10 H15 N3 O4' _chem_comp.formula_weight 241.244 _chem_comp.id MCY _chem_comp.mon_nstd_flag n _chem_comp.name "5-METHYL-2'-DEOXYCYTIDINE" _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 N1 C2 MCY sing 262 n n N1 C6 MCY sing 263 n n N1 C1' MCY sing 264 n n C2 N3 MCY sing 265 n n C2 O2 MCY doub 266 n n N3 C4 MCY doub 267 n n C4 C5 MCY sing 268 n n C4 N4 MCY sing 269 n n C5 C6 MCY doub 270 n n C5 C5A MCY sing 271 n n C6 H6 MCY sing 272 n n N4 HN41 MCY sing 273 n n N4 HN42 MCY sing 274 n n C1' C2' MCY sing 275 n n C1' O4' MCY sing 276 n n C1' H1' MCY sing 277 n n C2' C3' MCY sing 278 n n C2' H2' MCY sing 279 n n C2' "H2''" MCY sing 280 n n C3' C4' MCY sing 281 n n C3' O3' MCY sing 282 n n C3' H3' MCY sing 283 n n C4' O4' MCY sing 284 n n C4' C5' MCY sing 285 n n C4' H4' MCY sing 286 n n O3' HO3' MCY sing 287 n n C5' O5' MCY sing 288 n n C5' H5' MCY sing 289 n n C5' "H5''" MCY sing 290 n n O5' HO5' MCY sing 291 n n C5A H5A1 MCY sing 292 n n C5A H5A2 MCY sing 293 n n C5A H5A3 MCY sing 294 n n # _atom_sites.entry_id 3KFX _atom_sites.fract_transf_matrix[1][1] 0.018961 _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] 0.007522 _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] 0.006374 _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 ADP A 1 401 401 ADP ADP . D 3 MCY A 1 402 402 MCY MCY . E 2 ADP B 1 501 501 ADP ADP . F 3 MCY B 1 502 502 MCY MCY . G 4 HOH A 1 261 1 HOH HOH . G 4 HOH A 2 262 2 HOH HOH . G 4 HOH A 3 263 3 HOH HOH . G 4 HOH A 4 264 4 HOH HOH . G 4 HOH A 5 265 5 HOH HOH . G 4 HOH A 6 266 6 HOH HOH . G 4 HOH A 7 267 7 HOH HOH . G 4 HOH A 8 268 8 HOH HOH . G 4 HOH A 9 269 9 HOH HOH . G 4 HOH A 10 270 10 HOH HOH . G 4 HOH A 11 271 11 HOH HOH . G 4 HOH A 12 272 12 HOH HOH . G 4 HOH A 13 273 13 HOH HOH . G 4 HOH A 14 274 14 HOH HOH . G 4 HOH A 15 275 15 HOH HOH . G 4 HOH A 16 276 16 HOH HOH . G 4 HOH A 17 277 17 HOH HOH . G 4 HOH A 18 278 18 HOH HOH . G 4 HOH A 19 279 19 HOH HOH . G 4 HOH A 20 280 20 HOH HOH . G 4 HOH A 21 281 21 HOH HOH . G 4 HOH A 22 282 22 HOH HOH . G 4 HOH A 23 283 23 HOH HOH . G 4 HOH A 24 284 24 HOH HOH . G 4 HOH A 25 285 25 HOH HOH . G 4 HOH A 26 286 28 HOH HOH . G 4 HOH A 27 287 29 HOH HOH . G 4 HOH A 28 288 30 HOH HOH . G 4 HOH A 29 289 31 HOH HOH . G 4 HOH A 30 290 32 HOH HOH . G 4 HOH A 31 291 33 HOH HOH . G 4 HOH A 32 292 34 HOH HOH . G 4 HOH A 33 293 35 HOH HOH . G 4 HOH A 34 294 36 HOH HOH . G 4 HOH A 35 295 37 HOH HOH . G 4 HOH A 36 296 38 HOH HOH . G 4 HOH A 37 297 39 HOH HOH . G 4 HOH A 38 298 40 HOH HOH . G 4 HOH A 39 299 41 HOH HOH . G 4 HOH A 40 300 42 HOH HOH . G 4 HOH A 41 301 43 HOH HOH . G 4 HOH A 42 302 44 HOH HOH . G 4 HOH A 43 303 45 HOH HOH . G 4 HOH A 44 304 46 HOH HOH . G 4 HOH A 45 305 47 HOH HOH . G 4 HOH A 46 306 48 HOH HOH . G 4 HOH A 47 307 49 HOH HOH . G 4 HOH A 48 308 50 HOH HOH . G 4 HOH A 49 309 51 HOH HOH . G 4 HOH A 50 310 52 HOH HOH . G 4 HOH A 51 311 53 HOH HOH . G 4 HOH A 52 312 54 HOH HOH . G 4 HOH A 53 313 55 HOH HOH . G 4 HOH A 54 314 56 HOH HOH . G 4 HOH A 55 315 58 HOH HOH . G 4 HOH A 56 316 61 HOH HOH . G 4 HOH A 57 318 63 HOH HOH . G 4 HOH A 58 319 64 HOH HOH . G 4 HOH A 59 320 65 HOH HOH . G 4 HOH A 60 321 66 HOH HOH . G 4 HOH A 61 322 67 HOH HOH . G 4 HOH A 62 323 68 HOH HOH . G 4 HOH A 63 325 70 HOH HOH . G 4 HOH A 64 326 71 HOH HOH . G 4 HOH A 65 327 72 HOH HOH . G 4 HOH A 66 328 73 HOH HOH . G 4 HOH A 67 330 75 HOH HOH . G 4 HOH A 68 331 77 HOH HOH . G 4 HOH A 69 332 78 HOH HOH . G 4 HOH A 70 333 79 HOH HOH . G 4 HOH A 71 334 80 HOH HOH . G 4 HOH A 72 335 81 HOH HOH . G 4 HOH A 73 336 82 HOH HOH . G 4 HOH A 74 337 83 HOH HOH . G 4 HOH A 75 338 84 HOH HOH . G 4 HOH A 76 339 85 HOH HOH . G 4 HOH A 77 340 86 HOH HOH . G 4 HOH A 78 341 87 HOH HOH . G 4 HOH A 79 342 88 HOH HOH . G 4 HOH A 80 343 89 HOH HOH . G 4 HOH A 81 344 90 HOH HOH . G 4 HOH A 82 345 91 HOH HOH . G 4 HOH A 83 346 92 HOH HOH . G 4 HOH A 84 347 93 HOH HOH . G 4 HOH A 85 349 95 HOH HOH . G 4 HOH A 86 350 96 HOH HOH . G 4 HOH A 87 351 97 HOH HOH . G 4 HOH A 88 352 98 HOH HOH . G 4 HOH A 89 353 99 HOH HOH . G 4 HOH A 90 354 100 HOH HOH . G 4 HOH A 91 356 102 HOH HOH . G 4 HOH A 92 357 103 HOH HOH . G 4 HOH A 93 358 104 HOH HOH . G 4 HOH A 94 359 105 HOH HOH . G 4 HOH A 95 360 106 HOH HOH . G 4 HOH A 96 361 107 HOH HOH . G 4 HOH A 97 363 109 HOH HOH . G 4 HOH A 98 364 110 HOH HOH . G 4 HOH A 99 365 111 HOH HOH . G 4 HOH A 100 366 112 HOH HOH . G 4 HOH A 101 367 113 HOH HOH . G 4 HOH A 102 368 114 HOH HOH . G 4 HOH A 103 369 116 HOH HOH . G 4 HOH A 104 370 159 HOH HOH . G 4 HOH A 105 371 205 HOH HOH . G 4 HOH A 106 372 206 HOH HOH . G 4 HOH A 107 373 207 HOH HOH . G 4 HOH A 108 374 208 HOH HOH . G 4 HOH A 109 375 209 HOH HOH . G 4 HOH A 110 376 210 HOH HOH . G 4 HOH A 111 377 211 HOH HOH . G 4 HOH A 112 378 213 HOH HOH . G 4 HOH A 113 379 214 HOH HOH . G 4 HOH A 114 380 215 HOH HOH . G 4 HOH A 115 381 216 HOH HOH . G 4 HOH A 116 382 217 HOH HOH . G 4 HOH A 117 383 218 HOH HOH . G 4 HOH A 118 384 219 HOH HOH . G 4 HOH A 119 385 220 HOH HOH . G 4 HOH A 120 386 221 HOH HOH . G 4 HOH A 121 387 222 HOH HOH . G 4 HOH A 122 388 233 HOH HOH . H 4 HOH B 1 261 27 HOH HOH . H 4 HOH B 2 262 57 HOH HOH . H 4 HOH B 3 263 59 HOH HOH . H 4 HOH B 4 264 60 HOH HOH . H 4 HOH B 5 265 115 HOH HOH . H 4 HOH B 6 266 117 HOH HOH . H 4 HOH B 7 267 118 HOH HOH . H 4 HOH B 8 268 119 HOH HOH . H 4 HOH B 9 269 120 HOH HOH . H 4 HOH B 10 270 121 HOH HOH . H 4 HOH B 11 271 122 HOH HOH . H 4 HOH B 12 272 123 HOH HOH . H 4 HOH B 13 273 124 HOH HOH . H 4 HOH B 14 274 125 HOH HOH . H 4 HOH B 15 275 126 HOH HOH . H 4 HOH B 16 276 127 HOH HOH . H 4 HOH B 17 277 128 HOH HOH . H 4 HOH B 18 278 129 HOH HOH . H 4 HOH B 19 279 130 HOH HOH . H 4 HOH B 20 280 131 HOH HOH . H 4 HOH B 21 281 132 HOH HOH . H 4 HOH B 22 282 133 HOH HOH . H 4 HOH B 23 283 134 HOH HOH . H 4 HOH B 24 284 135 HOH HOH . H 4 HOH B 25 285 136 HOH HOH . H 4 HOH B 26 286 137 HOH HOH . H 4 HOH B 27 287 138 HOH HOH . H 4 HOH B 28 288 139 HOH HOH . H 4 HOH B 29 289 140 HOH HOH . H 4 HOH B 30 290 141 HOH HOH . H 4 HOH B 31 291 142 HOH HOH . H 4 HOH B 32 292 143 HOH HOH . H 4 HOH B 33 293 144 HOH HOH . H 4 HOH B 34 294 145 HOH HOH . H 4 HOH B 35 295 146 HOH HOH . H 4 HOH B 36 296 147 HOH HOH . H 4 HOH B 37 297 148 HOH HOH . H 4 HOH B 38 298 149 HOH HOH . H 4 HOH B 39 299 150 HOH HOH . H 4 HOH B 40 300 151 HOH HOH . H 4 HOH B 41 301 152 HOH HOH . H 4 HOH B 42 302 153 HOH HOH . H 4 HOH B 43 303 154 HOH HOH . H 4 HOH B 44 304 155 HOH HOH . H 4 HOH B 45 305 156 HOH HOH . H 4 HOH B 46 306 157 HOH HOH . H 4 HOH B 47 307 158 HOH HOH . H 4 HOH B 48 308 160 HOH HOH . H 4 HOH B 49 309 161 HOH HOH . H 4 HOH B 50 310 162 HOH HOH . H 4 HOH B 51 311 163 HOH HOH . H 4 HOH B 52 312 164 HOH HOH . H 4 HOH B 53 313 165 HOH HOH . H 4 HOH B 54 314 166 HOH HOH . H 4 HOH B 55 315 167 HOH HOH . H 4 HOH B 56 316 168 HOH HOH . H 4 HOH B 57 317 62 HOH HOH . H 4 HOH B 58 318 170 HOH HOH . H 4 HOH B 59 319 171 HOH HOH . H 4 HOH B 60 320 172 HOH HOH . H 4 HOH B 61 321 173 HOH HOH . H 4 HOH B 62 322 174 HOH HOH . H 4 HOH B 63 323 175 HOH HOH . H 4 HOH B 64 324 69 HOH HOH . H 4 HOH B 65 325 177 HOH HOH . H 4 HOH B 66 326 178 HOH HOH . H 4 HOH B 67 327 179 HOH HOH . H 4 HOH B 68 328 180 HOH HOH . H 4 HOH B 69 329 74 HOH HOH . H 4 HOH B 70 330 182 HOH HOH . H 4 HOH B 71 331 183 HOH HOH . H 4 HOH B 72 332 184 HOH HOH . H 4 HOH B 73 333 185 HOH HOH . H 4 HOH B 74 334 186 HOH HOH . H 4 HOH B 75 335 187 HOH HOH . H 4 HOH B 76 336 188 HOH HOH . H 4 HOH B 77 337 189 HOH HOH . H 4 HOH B 78 338 190 HOH HOH . H 4 HOH B 79 339 191 HOH HOH . H 4 HOH B 80 340 192 HOH HOH . H 4 HOH B 81 341 193 HOH HOH . H 4 HOH B 82 342 194 HOH HOH . H 4 HOH B 83 343 195 HOH HOH . H 4 HOH B 84 344 196 HOH HOH . H 4 HOH B 85 345 197 HOH HOH . H 4 HOH B 86 346 198 HOH HOH . H 4 HOH B 87 347 199 HOH HOH . H 4 HOH B 88 348 94 HOH HOH . H 4 HOH B 89 349 201 HOH HOH . H 4 HOH B 90 350 202 HOH HOH . H 4 HOH B 91 351 203 HOH HOH . H 4 HOH B 92 352 223 HOH HOH . H 4 HOH B 93 353 224 HOH HOH . H 4 HOH B 94 354 225 HOH HOH . H 4 HOH B 95 355 101 HOH HOH . H 4 HOH B 96 356 227 HOH HOH . H 4 HOH B 97 357 228 HOH HOH . H 4 HOH B 98 358 229 HOH HOH . H 4 HOH B 99 359 230 HOH HOH . H 4 HOH B 100 360 231 HOH HOH . H 4 HOH B 101 361 232 HOH HOH . H 4 HOH B 102 362 108 HOH HOH . H 4 HOH B 103 363 235 HOH HOH . H 4 HOH B 104 364 236 HOH HOH . H 4 HOH B 105 365 237 HOH HOH . H 4 HOH B 106 366 238 HOH HOH . H 4 HOH B 107 367 239 HOH HOH . H 4 HOH B 108 368 240 HOH HOH . H 4 HOH B 109 369 241 HOH HOH . H 4 HOH B 110 370 242 HOH HOH . H 4 HOH B 111 371 243 HOH HOH . H 4 HOH B 112 372 244 HOH HOH . H 4 HOH B 113 373 245 HOH HOH . H 4 HOH B 114 374 246 HOH HOH . H 4 HOH B 115 375 247 HOH HOH . H 4 HOH B 116 376 248 HOH HOH . H 4 HOH B 117 377 249 HOH HOH . H 4 HOH B 118 378 250 HOH HOH . H 4 HOH B 119 379 251 HOH HOH . H 4 HOH B 120 380 252 HOH HOH . H 4 HOH B 121 381 253 HOH HOH . H 4 HOH B 122 382 254 HOH HOH . H 4 HOH B 123 383 255 HOH HOH . H 4 HOH B 124 384 256 HOH HOH . H 4 HOH B 125 385 257 HOH HOH . H 4 HOH B 126 386 169 HOH HOH . H 4 HOH B 127 387 176 HOH HOH . H 4 HOH B 128 388 181 HOH HOH . H 4 HOH B 129 389 200 HOH HOH . H 4 HOH B 130 390 226 HOH HOH . H 4 HOH B 131 391 234 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 N N1 MCY . . . D 3 -10.633 26.932 -15.696 1 21.46 ? N1 MCY 402 A 1 HETATM 2 C C2 MCY . . . D 3 -11.537 26.131 -15.134 1 19.9 ? C2 MCY 402 A 1 HETATM 3 N N3 MCY . . . D 3 -11.175 24.931 -14.629 1 18.95 ? N3 MCY 402 A 1 HETATM 4 C C4 MCY . . . D 3 -9.872 24.521 -14.654 1 20.56 ? C4 MCY 402 A 1 HETATM 5 C C5 MCY . . . D 3 -8.926 25.34 -15.23 1 20.55 ? C5 MCY 402 A 1 HETATM 6 C C6 MCY . . . D 3 -9.333 26.565 -15.761 1 21.75 ? C6 MCY 402 A 1 HETATM 7 O O2 MCY . . . D 3 -12.831 26.552 -15.063 1 21.53 ? O2 MCY 402 A 1 HETATM 8 N N4 MCY . . . D 3 -9.514 23.312 -14.158 1 21.41 ? N4 MCY 402 A 1 HETATM 9 C C1' MCY . . . D 3 -11.053 28.195 -16.316 1 21.81 ? C1' MCY 402 A 1 HETATM 10 C C2' MCY . . . D 3 -10.553 29.485 -15.716 1 22.34 ? C2' MCY 402 A 1 HETATM 11 C C3' MCY . . . D 3 -10.343 30.384 -16.945 1 21.68 ? C3' MCY 402 A 1 HETATM 12 C C4' MCY . . . D 3 -10.006 29.447 -18.09 1 22.21 ? C4' MCY 402 A 1 HETATM 13 O O4' MCY . . . D 3 -10.501 28.167 -17.668 1 21.76 ? O4' MCY 402 A 1 HETATM 14 O O3' MCY . . . D 3 -11.57 30.989 -17.331 1 22.38 ? O3' MCY 402 A 1 HETATM 15 C C5' MCY . . . D 3 -8.511 29.482 -18.441 1 19.68 ? C5' MCY 402 A 1 HETATM 16 O O5' MCY . . . D 3 -7.785 29.084 -17.28 1 19.24 ? O5' MCY 402 A 1 HETATM 17 C C5A MCY . . . D 3 -7.479 24.96 -15.308 1 21.22 ? C5A MCY 402 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 17 #