data_5KM9 # _model_server_result.job_id 8xqdqowND3r8kJeIE11JFA _model_server_result.datetime_utc '2024-11-05 01:25:55' _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 5km9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 5KM9 # _exptl.entry_id 5KM9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 267.241 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ADENOSINE _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 5KM9 _cell.length_a 37.753 _cell.length_b 74.771 _cell.length_c 77.863 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KM9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,E,F,G,H _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 C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H13 N5 O4' _chem_comp.formula_weight 267.241 _chem_comp.id ADN _chem_comp.mon_nstd_flag . _chem_comp.name ADENOSINE _chem_comp.type non-polymer _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 O5' C5' ADN sing 1 n n O5' HO5' ADN sing 2 n n C5' C4' ADN sing 3 n n C5' "H5'1" ADN sing 4 n n C5' "H5'2" ADN sing 5 n n C4' O4' ADN sing 6 n n C4' C3' ADN sing 7 n n C4' H4' ADN sing 8 n n O4' C1' ADN sing 9 n n C3' O3' ADN sing 10 n n C3' C2' ADN sing 11 n n C3' H3' ADN sing 12 n n O3' HO3' ADN sing 13 n n C2' O2' ADN sing 14 n n C2' C1' ADN sing 15 n n C2' H2' ADN sing 16 n n O2' HO2' ADN sing 17 n n C1' N9 ADN sing 18 n n C1' H1' ADN sing 19 n n N9 C8 ADN sing 20 n y N9 C4 ADN sing 21 n y C8 N7 ADN doub 22 n y C8 H8 ADN sing 23 n n N7 C5 ADN sing 24 n y C5 C6 ADN sing 25 n y C5 C4 ADN doub 26 n y C6 N6 ADN sing 27 n n C6 N1 ADN doub 28 n y N6 HN61 ADN sing 29 n n N6 HN62 ADN sing 30 n n N1 C2 ADN sing 31 n y C2 N3 ADN doub 32 n y C2 H2 ADN sing 33 n n N3 C4 ADN sing 34 n y # _atom_sites.entry_id 5KM9 _atom_sites.fract_transf_matrix[1][1] 0.026488 _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] 0.013374 _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] 0.012843 _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 ADN B 1 201 164 ADN ADN . D 3 PG4 B 1 202 165 PG4 PG4 . E 4 GOL B 1 203 1 GOL GOL . F 5 CL A 1 201 164 CL CL . G 6 HOH B 1 301 270 HOH HOH . G 6 HOH B 2 302 256 HOH HOH . G 6 HOH B 3 303 225 HOH HOH . G 6 HOH B 4 304 271 HOH HOH . G 6 HOH B 5 305 199 HOH HOH . G 6 HOH B 6 306 227 HOH HOH . G 6 HOH B 7 307 203 HOH HOH . G 6 HOH B 8 308 248 HOH HOH . G 6 HOH B 9 309 184 HOH HOH . G 6 HOH B 10 310 193 HOH HOH . G 6 HOH B 11 311 277 HOH HOH . G 6 HOH B 12 312 191 HOH HOH . G 6 HOH B 13 313 176 HOH HOH . G 6 HOH B 14 314 192 HOH HOH . G 6 HOH B 15 315 174 HOH HOH . G 6 HOH B 16 316 217 HOH HOH . G 6 HOH B 17 317 295 HOH HOH . G 6 HOH B 18 318 172 HOH HOH . G 6 HOH B 19 319 246 HOH HOH . G 6 HOH B 20 320 243 HOH HOH . G 6 HOH B 21 321 204 HOH HOH . G 6 HOH B 22 322 189 HOH HOH . G 6 HOH B 23 323 210 HOH HOH . G 6 HOH B 24 324 224 HOH HOH . G 6 HOH B 25 325 166 HOH HOH . G 6 HOH B 26 326 208 HOH HOH . G 6 HOH B 27 327 252 HOH HOH . G 6 HOH B 28 328 187 HOH HOH . G 6 HOH B 29 329 263 HOH HOH . G 6 HOH B 30 330 220 HOH HOH . G 6 HOH B 31 331 168 HOH HOH . G 6 HOH B 32 332 273 HOH HOH . G 6 HOH B 33 333 237 HOH HOH . G 6 HOH B 34 334 236 HOH HOH . G 6 HOH B 35 335 265 HOH HOH . G 6 HOH B 36 336 173 HOH HOH . G 6 HOH B 37 337 206 HOH HOH . G 6 HOH B 38 338 179 HOH HOH . G 6 HOH B 39 339 216 HOH HOH . G 6 HOH B 40 340 245 HOH HOH . G 6 HOH B 41 341 171 HOH HOH . G 6 HOH B 42 342 278 HOH HOH . G 6 HOH B 43 343 266 HOH HOH . G 6 HOH B 44 344 169 HOH HOH . G 6 HOH B 45 345 180 HOH HOH . G 6 HOH B 46 346 175 HOH HOH . G 6 HOH B 47 347 254 HOH HOH . G 6 HOH B 48 348 275 HOH HOH . G 6 HOH B 49 349 186 HOH HOH . G 6 HOH B 50 350 198 HOH HOH . G 6 HOH B 51 351 259 HOH HOH . G 6 HOH B 52 352 181 HOH HOH . G 6 HOH B 53 353 280 HOH HOH . G 6 HOH B 54 354 292 HOH HOH . G 6 HOH B 55 355 182 HOH HOH . G 6 HOH B 56 356 262 HOH HOH . G 6 HOH B 57 357 261 HOH HOH . G 6 HOH B 58 358 257 HOH HOH . G 6 HOH B 59 359 9 HOH HOH . G 6 HOH B 60 360 177 HOH HOH . G 6 HOH B 61 361 201 HOH HOH . G 6 HOH B 62 362 228 HOH HOH . G 6 HOH B 63 363 202 HOH HOH . G 6 HOH B 64 364 223 HOH HOH . G 6 HOH B 65 365 3 HOH HOH . G 6 HOH B 66 366 253 HOH HOH . G 6 HOH B 67 367 214 HOH HOH . G 6 HOH B 68 368 241 HOH HOH . G 6 HOH B 69 369 200 HOH HOH . G 6 HOH B 70 370 215 HOH HOH . G 6 HOH B 71 371 196 HOH HOH . G 6 HOH B 72 372 269 HOH HOH . G 6 HOH B 73 373 181 HOH HOH . G 6 HOH B 74 374 301 HOH HOH . G 6 HOH B 75 375 209 HOH HOH . G 6 HOH B 76 376 170 HOH HOH . G 6 HOH B 77 377 2 HOH HOH . G 6 HOH B 78 378 188 HOH HOH . G 6 HOH B 79 379 195 HOH HOH . G 6 HOH B 80 380 190 HOH HOH . G 6 HOH B 81 381 194 HOH HOH . G 6 HOH B 82 382 178 HOH HOH . G 6 HOH B 83 383 255 HOH HOH . G 6 HOH B 84 384 185 HOH HOH . G 6 HOH B 85 385 240 HOH HOH . G 6 HOH B 86 386 207 HOH HOH . G 6 HOH B 87 387 197 HOH HOH . G 6 HOH B 88 388 213 HOH HOH . G 6 HOH B 89 389 260 HOH HOH . G 6 HOH B 90 390 167 HOH HOH . G 6 HOH B 91 391 212 HOH HOH . G 6 HOH B 92 392 178 HOH HOH . G 6 HOH B 93 393 290 HOH HOH . G 6 HOH B 94 394 293 HOH HOH . G 6 HOH B 95 395 221 HOH HOH . G 6 HOH B 96 396 222 HOH HOH . G 6 HOH B 97 397 226 HOH HOH . G 6 HOH B 98 398 250 HOH HOH . G 6 HOH B 99 399 267 HOH HOH . G 6 HOH B 100 400 285 HOH HOH . G 6 HOH B 101 401 234 HOH HOH . G 6 HOH B 102 402 279 HOH HOH . G 6 HOH B 103 403 272 HOH HOH . G 6 HOH B 104 404 211 HOH HOH . G 6 HOH B 105 405 183 HOH HOH . G 6 HOH B 106 406 296 HOH HOH . G 6 HOH B 107 407 274 HOH HOH . G 6 HOH B 108 408 235 HOH HOH . G 6 HOH B 109 409 5 HOH HOH . G 6 HOH B 110 410 230 HOH HOH . G 6 HOH B 111 411 297 HOH HOH . G 6 HOH B 112 412 264 HOH HOH . G 6 HOH B 113 413 282 HOH HOH . G 6 HOH B 114 414 229 HOH HOH . G 6 HOH B 115 415 238 HOH HOH . G 6 HOH B 116 416 234 HOH HOH . G 6 HOH B 117 417 284 HOH HOH . G 6 HOH B 118 418 219 HOH HOH . G 6 HOH B 119 419 283 HOH HOH . G 6 HOH B 120 420 205 HOH HOH . G 6 HOH B 121 421 251 HOH HOH . G 6 HOH B 122 422 233 HOH HOH . G 6 HOH B 123 423 247 HOH HOH . G 6 HOH B 124 424 249 HOH HOH . G 6 HOH B 125 425 239 HOH HOH . G 6 HOH B 126 426 232 HOH HOH . G 6 HOH B 127 427 286 HOH HOH . G 6 HOH B 128 428 258 HOH HOH . G 6 HOH B 129 429 299 HOH HOH . G 6 HOH B 130 430 281 HOH HOH . H 6 HOH A 1 301 227 HOH HOH . H 6 HOH A 2 302 251 HOH HOH . H 6 HOH A 3 303 247 HOH HOH . H 6 HOH A 4 304 242 HOH HOH . H 6 HOH A 5 305 214 HOH HOH . H 6 HOH A 6 306 256 HOH HOH . H 6 HOH A 7 307 246 HOH HOH . H 6 HOH A 8 308 236 HOH HOH . H 6 HOH A 9 309 235 HOH HOH . H 6 HOH A 10 310 184 HOH HOH . H 6 HOH A 11 311 273 HOH HOH . H 6 HOH A 12 312 211 HOH HOH . H 6 HOH A 13 313 278 HOH HOH . H 6 HOH A 14 314 231 HOH HOH . H 6 HOH A 15 315 194 HOH HOH . H 6 HOH A 16 316 182 HOH HOH . H 6 HOH A 17 317 222 HOH HOH . H 6 HOH A 18 318 238 HOH HOH . H 6 HOH A 19 319 219 HOH HOH . H 6 HOH A 20 320 223 HOH HOH . H 6 HOH A 21 321 224 HOH HOH . H 6 HOH A 22 322 199 HOH HOH . H 6 HOH A 23 323 169 HOH HOH . H 6 HOH A 24 324 167 HOH HOH . H 6 HOH A 25 325 255 HOH HOH . H 6 HOH A 26 326 220 HOH HOH . H 6 HOH A 27 327 207 HOH HOH . H 6 HOH A 28 328 197 HOH HOH . H 6 HOH A 29 329 187 HOH HOH . H 6 HOH A 30 330 191 HOH HOH . H 6 HOH A 31 331 172 HOH HOH . H 6 HOH A 32 332 185 HOH HOH . H 6 HOH A 33 333 204 HOH HOH . H 6 HOH A 34 334 217 HOH HOH . H 6 HOH A 35 335 171 HOH HOH . H 6 HOH A 36 336 196 HOH HOH . H 6 HOH A 37 337 174 HOH HOH . H 6 HOH A 38 338 209 HOH HOH . H 6 HOH A 39 339 165 HOH HOH . H 6 HOH A 40 340 193 HOH HOH . H 6 HOH A 41 341 263 HOH HOH . H 6 HOH A 42 342 190 HOH HOH . H 6 HOH A 43 343 221 HOH HOH . H 6 HOH A 44 344 228 HOH HOH . H 6 HOH A 45 345 189 HOH HOH . H 6 HOH A 46 346 177 HOH HOH . H 6 HOH A 47 347 173 HOH HOH . H 6 HOH A 48 348 170 HOH HOH . H 6 HOH A 49 349 203 HOH HOH . H 6 HOH A 50 350 183 HOH HOH . H 6 HOH A 51 351 253 HOH HOH . H 6 HOH A 52 352 216 HOH HOH . H 6 HOH A 53 353 240 HOH HOH . H 6 HOH A 54 354 195 HOH HOH . H 6 HOH A 55 355 8 HOH HOH . H 6 HOH A 56 356 218 HOH HOH . H 6 HOH A 57 357 213 HOH HOH . H 6 HOH A 58 358 186 HOH HOH . H 6 HOH A 59 359 239 HOH HOH . H 6 HOH A 60 360 168 HOH HOH . H 6 HOH A 61 361 188 HOH HOH . H 6 HOH A 62 362 192 HOH HOH . H 6 HOH A 63 363 166 HOH HOH . H 6 HOH A 64 364 200 HOH HOH . H 6 HOH A 65 365 210 HOH HOH . H 6 HOH A 66 366 232 HOH HOH . H 6 HOH A 67 367 279 HOH HOH . H 6 HOH A 68 368 179 HOH HOH . H 6 HOH A 69 369 241 HOH HOH . H 6 HOH A 70 370 176 HOH HOH . H 6 HOH A 71 371 175 HOH HOH . H 6 HOH A 72 372 215 HOH HOH . H 6 HOH A 73 373 208 HOH HOH . H 6 HOH A 74 374 1 HOH HOH . H 6 HOH A 75 375 198 HOH HOH . H 6 HOH A 76 376 205 HOH HOH . H 6 HOH A 77 377 277 HOH HOH . H 6 HOH A 78 378 252 HOH HOH . H 6 HOH A 79 379 269 HOH HOH . H 6 HOH A 80 380 245 HOH HOH . H 6 HOH A 81 381 265 HOH HOH . H 6 HOH A 82 382 202 HOH HOH . H 6 HOH A 83 383 267 HOH HOH . H 6 HOH A 84 384 180 HOH HOH . H 6 HOH A 85 385 250 HOH HOH . H 6 HOH A 86 386 254 HOH HOH . H 6 HOH A 87 387 7 HOH HOH . H 6 HOH A 88 388 264 HOH HOH . H 6 HOH A 89 389 258 HOH HOH . H 6 HOH A 90 390 244 HOH HOH . H 6 HOH A 91 391 237 HOH HOH . H 6 HOH A 92 392 230 HOH HOH . H 6 HOH A 93 393 226 HOH HOH . H 6 HOH A 94 394 201 HOH HOH . H 6 HOH A 95 395 272 HOH HOH . H 6 HOH A 96 396 6 HOH HOH . H 6 HOH A 97 397 248 HOH HOH . H 6 HOH A 98 398 233 HOH HOH . H 6 HOH A 99 399 243 HOH HOH . H 6 HOH A 100 400 268 HOH HOH . H 6 HOH A 101 401 268 HOH HOH . H 6 HOH A 102 402 10 HOH HOH . H 6 HOH A 103 403 275 HOH HOH . H 6 HOH A 104 404 231 HOH HOH . H 6 HOH A 105 405 287 HOH HOH . H 6 HOH A 106 406 261 HOH HOH . H 6 HOH A 107 407 212 HOH HOH . H 6 HOH A 108 408 225 HOH HOH . H 6 HOH A 109 409 4 HOH HOH . H 6 HOH A 110 410 206 HOH HOH . H 6 HOH A 111 411 260 HOH HOH . H 6 HOH A 112 412 276 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 O5' ADN . . . C 2 -11.338 -0.491 3.135 1 24.82 ? O5' ADN 201 B 1 HETATM 2 C C5' ADN . . . C 2 -10.856 -0.563 1.792 1 19.7 ? C5' ADN 201 B 1 HETATM 3 C C4' ADN . . . C 2 -10.834 -1.986 1.293 1 16.68 ? C4' ADN 201 B 1 HETATM 4 O O4' ADN . . . C 2 -9.718 -2.669 1.932 1 17.56 ? O4' ADN 201 B 1 HETATM 5 C C3' ADN . . . C 2 -12.094 -2.8 1.634 1 15.29 ? C3' ADN 201 B 1 HETATM 6 O O3' ADN . . . C 2 -12.459 -3.654 0.542 1 15.16 ? O3' ADN 201 B 1 HETATM 7 C C2' ADN . . . C 2 -11.644 -3.632 2.837 1 16.27 ? C2' ADN 201 B 1 HETATM 8 O O2' ADN . . . C 2 -12.325 -4.855 3.036 1 16.1 ? O2' ADN 201 B 1 HETATM 9 C C1' ADN . . . C 2 -10.174 -3.862 2.527 1 15.21 ? C1' ADN 201 B 1 HETATM 10 N N9 ADN . . . C 2 -9.393 -4.13 3.735 1 16.55 ? N9 ADN 201 B 1 HETATM 11 C C8 ADN . . . C 2 -9.441 -3.431 4.892 1 16.63 ? C8 ADN 201 B 1 HETATM 12 N N7 ADN . . . C 2 -8.616 -3.978 5.819 1 16.49 ? N7 ADN 201 B 1 HETATM 13 C C5 ADN . . . C 2 -8.032 -5.051 5.258 1 17.46 ? C5 ADN 201 B 1 HETATM 14 C C6 ADN . . . C 2 -7.062 -6.076 5.682 1 17.4 ? C6 ADN 201 B 1 HETATM 15 N N6 ADN . . . C 2 -6.535 -6.058 6.924 1 18.96 ? N6 ADN 201 B 1 HETATM 16 N N1 ADN . . . C 2 -6.717 -7.021 4.785 1 16.01 ? N1 ADN 201 B 1 HETATM 17 C C2 ADN . . . C 2 -7.239 -7.05 3.545 1 14.86 ? C2 ADN 201 B 1 HETATM 18 N N3 ADN . . . C 2 -8.136 -6.162 3.093 1 15.78 ? N3 ADN 201 B 1 HETATM 19 C C4 ADN . . . C 2 -8.555 -5.151 3.894 1 16.15 ? C4 ADN 201 B 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 120 _model_server_stats.create_model_time_ms 71 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 19 #