data_2ZVB # _model_server_result.job_id UPMRpmTi5B8ZF-k1hG6lbw _model_server_result.datetime_utc '2025-08-31 11:40:20' _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 2zvb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 2ZVB # _exptl.entry_id 2ZVB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _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 2ZVB _cell.length_a 61.318 _cell.length_b 86.456 _cell.length_c 126.343 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZVB _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 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 _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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 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 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag n _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type 'l-peptide 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 N CA SAH sing 277 n n N HN1 SAH sing 278 n n N HN2 SAH sing 279 n n CA CB SAH sing 280 n n CA C SAH sing 281 n n CA HA SAH sing 282 n n CB CG SAH sing 283 n n CB HB1 SAH sing 284 n n CB HB2 SAH sing 285 n n CG SD SAH sing 286 n n CG HG1 SAH sing 287 n n CG HG2 SAH sing 288 n n SD C5' SAH sing 289 n n C O SAH doub 290 n n C OXT SAH sing 291 n n OXT HXT SAH sing 292 n n C5' C4' SAH sing 293 n n C5' "H5'1" SAH sing 294 n n C5' "H5'2" SAH sing 295 n n C4' O4' SAH sing 296 n n C4' C3' SAH sing 297 n n C4' H4' SAH sing 298 n n O4' C1' SAH sing 299 n n C3' O3' SAH sing 300 n n C3' C2' SAH sing 301 n n C3' H3' SAH sing 302 n n O3' HO3' SAH sing 303 n n C2' O2' SAH sing 304 n n C2' C1' SAH sing 305 n n C2' H2' SAH sing 306 n n O2' HO2' SAH sing 307 n n C1' N9 SAH sing 308 n n C1' H1' SAH sing 309 n n N9 C8 SAH sing 310 n y N9 C4 SAH sing 311 n y C8 N7 SAH doub 312 n y C8 H8 SAH sing 313 n n N7 C5 SAH sing 314 n y C5 C6 SAH sing 315 n y C5 C4 SAH doub 316 n y C6 N6 SAH sing 317 n n C6 N1 SAH doub 318 n y N6 HN61 SAH sing 319 n n N6 HN62 SAH sing 320 n n N1 C2 SAH sing 321 n y C2 N3 SAH doub 322 n y C2 H2 SAH sing 323 n n N3 C4 SAH sing 324 n y # _atom_sites.entry_id 2ZVB _atom_sites.fract_transf_matrix[1][1] 0.016308 _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] 0.011567 _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] 0.007915 _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 SAH A 1 301 301 SAH SAH . C 3 HOH A 1 296 1 HOH HOH . C 3 HOH A 2 297 2 HOH HOH . C 3 HOH A 3 298 3 HOH HOH . C 3 HOH A 4 299 4 HOH HOH . C 3 HOH A 5 300 5 HOH HOH . C 3 HOH A 6 302 6 HOH HOH . C 3 HOH A 7 303 7 HOH HOH . C 3 HOH A 8 304 8 HOH HOH . C 3 HOH A 9 305 9 HOH HOH . C 3 HOH A 10 306 10 HOH HOH . C 3 HOH A 11 307 11 HOH HOH . C 3 HOH A 12 308 13 HOH HOH . C 3 HOH A 13 309 14 HOH HOH . C 3 HOH A 14 310 15 HOH HOH . C 3 HOH A 15 311 16 HOH HOH . C 3 HOH A 16 312 17 HOH HOH . C 3 HOH A 17 313 18 HOH HOH . C 3 HOH A 18 314 19 HOH HOH . C 3 HOH A 19 315 20 HOH HOH . C 3 HOH A 20 316 21 HOH HOH . C 3 HOH A 21 317 22 HOH HOH . C 3 HOH A 22 318 23 HOH HOH . C 3 HOH A 23 319 24 HOH HOH . C 3 HOH A 24 320 25 HOH HOH . C 3 HOH A 25 321 26 HOH HOH . C 3 HOH A 26 322 27 HOH HOH . C 3 HOH A 27 323 28 HOH HOH . C 3 HOH A 28 324 29 HOH HOH . C 3 HOH A 29 325 30 HOH HOH . C 3 HOH A 30 326 31 HOH HOH . C 3 HOH A 31 327 32 HOH HOH . C 3 HOH A 32 328 33 HOH HOH . C 3 HOH A 33 329 34 HOH HOH . C 3 HOH A 34 330 35 HOH HOH . C 3 HOH A 35 331 36 HOH HOH . C 3 HOH A 36 332 37 HOH HOH . C 3 HOH A 37 333 38 HOH HOH . C 3 HOH A 38 334 39 HOH HOH . C 3 HOH A 39 335 40 HOH HOH . C 3 HOH A 40 336 41 HOH HOH . C 3 HOH A 41 337 42 HOH HOH . C 3 HOH A 42 338 43 HOH HOH . C 3 HOH A 43 339 44 HOH HOH . C 3 HOH A 44 340 45 HOH HOH . C 3 HOH A 45 341 46 HOH HOH . C 3 HOH A 46 342 47 HOH HOH . C 3 HOH A 47 343 48 HOH HOH . C 3 HOH A 48 344 49 HOH HOH . C 3 HOH A 49 345 51 HOH HOH . C 3 HOH A 50 346 52 HOH HOH . C 3 HOH A 51 347 53 HOH HOH . C 3 HOH A 52 348 54 HOH HOH . C 3 HOH A 53 349 55 HOH HOH . C 3 HOH A 54 350 56 HOH HOH . C 3 HOH A 55 351 57 HOH HOH . C 3 HOH A 56 352 59 HOH HOH . C 3 HOH A 57 353 60 HOH HOH . C 3 HOH A 58 354 61 HOH HOH . C 3 HOH A 59 355 62 HOH HOH . C 3 HOH A 60 356 63 HOH HOH . C 3 HOH A 61 357 64 HOH HOH . C 3 HOH A 62 358 65 HOH HOH . C 3 HOH A 63 359 66 HOH HOH . C 3 HOH A 64 360 69 HOH HOH . C 3 HOH A 65 361 70 HOH HOH . C 3 HOH A 66 362 71 HOH HOH . C 3 HOH A 67 363 72 HOH HOH . C 3 HOH A 68 364 73 HOH HOH . C 3 HOH A 69 365 74 HOH HOH . C 3 HOH A 70 366 75 HOH HOH . C 3 HOH A 71 367 76 HOH HOH . C 3 HOH A 72 368 77 HOH HOH . C 3 HOH A 73 369 79 HOH HOH . C 3 HOH A 74 370 80 HOH HOH . C 3 HOH A 75 371 81 HOH HOH . C 3 HOH A 76 372 82 HOH HOH . C 3 HOH A 77 373 83 HOH HOH . C 3 HOH A 78 374 85 HOH HOH . C 3 HOH A 79 375 86 HOH HOH . C 3 HOH A 80 376 87 HOH HOH . C 3 HOH A 81 377 88 HOH HOH . C 3 HOH A 82 378 90 HOH HOH . C 3 HOH A 83 379 91 HOH HOH . C 3 HOH A 84 380 92 HOH HOH . C 3 HOH A 85 381 93 HOH HOH . C 3 HOH A 86 382 94 HOH HOH . C 3 HOH A 87 383 95 HOH HOH . C 3 HOH A 88 384 96 HOH HOH . C 3 HOH A 89 385 97 HOH HOH . C 3 HOH A 90 386 98 HOH HOH . C 3 HOH A 91 387 99 HOH HOH . C 3 HOH A 92 388 100 HOH HOH . C 3 HOH A 93 389 101 HOH HOH . C 3 HOH A 94 390 102 HOH HOH . C 3 HOH A 95 391 104 HOH HOH . C 3 HOH A 96 392 105 HOH HOH . C 3 HOH A 97 393 106 HOH HOH . C 3 HOH A 98 394 107 HOH HOH . C 3 HOH A 99 395 108 HOH HOH . C 3 HOH A 100 396 109 HOH HOH . C 3 HOH A 101 397 112 HOH HOH . C 3 HOH A 102 398 113 HOH HOH . C 3 HOH A 103 399 114 HOH HOH . C 3 HOH A 104 400 116 HOH HOH . C 3 HOH A 105 401 117 HOH HOH . C 3 HOH A 106 402 118 HOH HOH . C 3 HOH A 107 403 119 HOH HOH . C 3 HOH A 108 404 121 HOH HOH . C 3 HOH A 109 405 122 HOH HOH . C 3 HOH A 110 406 123 HOH HOH . C 3 HOH A 111 407 124 HOH HOH . C 3 HOH A 112 408 125 HOH HOH . C 3 HOH A 113 409 126 HOH HOH . C 3 HOH A 114 410 127 HOH HOH . C 3 HOH A 115 411 128 HOH HOH . C 3 HOH A 116 412 129 HOH HOH . C 3 HOH A 117 413 131 HOH HOH . C 3 HOH A 118 414 132 HOH HOH . C 3 HOH A 119 415 133 HOH HOH . C 3 HOH A 120 416 134 HOH HOH . C 3 HOH A 121 417 135 HOH HOH . C 3 HOH A 122 418 136 HOH HOH . C 3 HOH A 123 419 137 HOH HOH . C 3 HOH A 124 420 138 HOH HOH . C 3 HOH A 125 421 139 HOH HOH . C 3 HOH A 126 422 140 HOH HOH . C 3 HOH A 127 423 141 HOH HOH . C 3 HOH A 128 424 142 HOH HOH . C 3 HOH A 129 425 143 HOH HOH . C 3 HOH A 130 426 145 HOH HOH . C 3 HOH A 131 427 146 HOH HOH . C 3 HOH A 132 428 147 HOH HOH . C 3 HOH A 133 429 148 HOH HOH . C 3 HOH A 134 430 149 HOH HOH . C 3 HOH A 135 431 151 HOH HOH . C 3 HOH A 136 432 152 HOH HOH . C 3 HOH A 137 433 153 HOH HOH . C 3 HOH A 138 434 154 HOH HOH . C 3 HOH A 139 435 155 HOH HOH . C 3 HOH A 140 436 156 HOH HOH . C 3 HOH A 141 437 159 HOH HOH . C 3 HOH A 142 438 160 HOH HOH . C 3 HOH A 143 439 161 HOH HOH . C 3 HOH A 144 440 162 HOH HOH . C 3 HOH A 145 441 163 HOH HOH . C 3 HOH A 146 442 165 HOH HOH . C 3 HOH A 147 443 166 HOH HOH . C 3 HOH A 148 444 167 HOH HOH . C 3 HOH A 149 445 172 HOH HOH . C 3 HOH A 150 446 173 HOH HOH . C 3 HOH A 151 447 174 HOH HOH . C 3 HOH A 152 448 175 HOH HOH . C 3 HOH A 153 449 176 HOH HOH . C 3 HOH A 154 450 178 HOH HOH . C 3 HOH A 155 451 179 HOH HOH . C 3 HOH A 156 452 180 HOH HOH . C 3 HOH A 157 453 184 HOH HOH . C 3 HOH A 158 454 185 HOH HOH . C 3 HOH A 159 455 186 HOH HOH . C 3 HOH A 160 456 187 HOH HOH . C 3 HOH A 161 457 188 HOH HOH . C 3 HOH A 162 458 190 HOH HOH . C 3 HOH A 163 459 191 HOH HOH . C 3 HOH A 164 460 192 HOH HOH . C 3 HOH A 165 461 193 HOH HOH . C 3 HOH A 166 462 194 HOH HOH . C 3 HOH A 167 463 196 HOH HOH . C 3 HOH A 168 464 197 HOH HOH . C 3 HOH A 169 465 198 HOH HOH . C 3 HOH A 170 466 199 HOH HOH . C 3 HOH A 171 467 200 HOH HOH . C 3 HOH A 172 468 201 HOH HOH . C 3 HOH A 173 469 203 HOH HOH . C 3 HOH A 174 470 204 HOH HOH . C 3 HOH A 175 471 205 HOH HOH . C 3 HOH A 176 472 211 HOH HOH . C 3 HOH A 177 473 213 HOH HOH . C 3 HOH A 178 474 215 HOH HOH . C 3 HOH A 179 475 216 HOH HOH . C 3 HOH A 180 476 218 HOH HOH . C 3 HOH A 181 477 221 HOH HOH . C 3 HOH A 182 478 222 HOH HOH . C 3 HOH A 183 479 223 HOH HOH . C 3 HOH A 184 480 224 HOH HOH . C 3 HOH A 185 481 225 HOH HOH . C 3 HOH A 186 482 226 HOH HOH . C 3 HOH A 187 483 227 HOH HOH . C 3 HOH A 188 484 228 HOH HOH . C 3 HOH A 189 485 229 HOH HOH . C 3 HOH A 190 486 230 HOH HOH . C 3 HOH A 191 487 234 HOH HOH . C 3 HOH A 192 488 235 HOH HOH . C 3 HOH A 193 489 236 HOH HOH . C 3 HOH A 194 490 237 HOH HOH . C 3 HOH A 195 491 241 HOH HOH . C 3 HOH A 196 492 244 HOH HOH . C 3 HOH A 197 493 245 HOH HOH . C 3 HOH A 198 494 246 HOH HOH . C 3 HOH A 199 495 247 HOH HOH . C 3 HOH A 200 496 248 HOH HOH . C 3 HOH A 201 497 249 HOH HOH . C 3 HOH A 202 498 250 HOH HOH . C 3 HOH A 203 499 251 HOH HOH . C 3 HOH A 204 500 252 HOH HOH . C 3 HOH A 205 501 253 HOH HOH . C 3 HOH A 206 502 254 HOH HOH . C 3 HOH A 207 503 255 HOH HOH . C 3 HOH A 208 504 256 HOH HOH . C 3 HOH A 209 505 257 HOH HOH . C 3 HOH A 210 506 258 HOH HOH . C 3 HOH A 211 507 259 HOH HOH . C 3 HOH A 212 508 260 HOH HOH . C 3 HOH A 213 509 261 HOH HOH . C 3 HOH A 214 510 262 HOH HOH . C 3 HOH A 215 511 263 HOH HOH . C 3 HOH A 216 512 264 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 N SAH . . . B 2 2.666 9.25 26.253 1 23.94 ? N SAH 301 A 1 HETATM 2 C CA SAH . . . B 2 1.168 9.503 26.146 1 21.7 ? CA SAH 301 A 1 HETATM 3 C CB SAH . . . B 2 0.677 10.292 24.969 1 24.95 ? CB SAH 301 A 1 HETATM 4 C CG SAH . . . B 2 1.224 11.693 24.728 1 28.6 ? CG SAH 301 A 1 HETATM 5 S SD SAH . . . B 2 0.321 12.398 23.277 1 29.2 ? SD SAH 301 A 1 HETATM 6 C C SAH . . . B 2 0.465 8.08 26.196 1 22.24 ? C SAH 301 A 1 HETATM 7 O O SAH . . . B 2 1.168 7.048 26.297 1 18.84 ? O SAH 301 A 1 HETATM 8 O OXT SAH . . . B 2 -0.826 8.087 26.136 1 18.29 ? OXT SAH 301 A 1 HETATM 9 C C5' SAH . . . B 2 -1.072 13.114 24.049 1 29.7 ? C5' SAH 301 A 1 HETATM 10 C C4' SAH . . . B 2 -2.371 12.487 23.395 1 28.79 ? C4' SAH 301 A 1 HETATM 11 O O4' SAH . . . B 2 -2.588 11.206 24.034 1 28.67 ? O4' SAH 301 A 1 HETATM 12 C C3' SAH . . . B 2 -3.631 13.259 23.572 1 29.7 ? C3' SAH 301 A 1 HETATM 13 O O3' SAH . . . B 2 -3.751 14.265 22.563 1 30.48 ? O3' SAH 301 A 1 HETATM 14 C C2' SAH . . . B 2 -4.685 12.126 23.496 1 29.68 ? C2' SAH 301 A 1 HETATM 15 O O2' SAH . . . B 2 -4.999 11.795 22.145 1 28.11 ? O2' SAH 301 A 1 HETATM 16 C C1' SAH . . . B 2 -4.049 10.958 24.273 1 28.87 ? C1' SAH 301 A 1 HETATM 17 N N9 SAH . . . B 2 -4.315 10.918 25.608 1 30.66 ? N9 SAH 301 A 1 HETATM 18 C C8 SAH . . . B 2 -3.54 11.052 26.745 1 30.01 ? C8 SAH 301 A 1 HETATM 19 N N7 SAH . . . B 2 -4.176 10.936 27.872 1 31.01 ? N7 SAH 301 A 1 HETATM 20 C C5 SAH . . . B 2 -5.528 10.696 27.498 1 30.73 ? C5 SAH 301 A 1 HETATM 21 C C6 SAH . . . B 2 -6.719 10.477 28.293 1 30.56 ? C6 SAH 301 A 1 HETATM 22 N N6 SAH . . . B 2 -6.733 10.46 29.637 1 29.69 ? N6 SAH 301 A 1 HETATM 23 N N1 SAH . . . B 2 -7.876 10.277 27.563 1 29.37 ? N1 SAH 301 A 1 HETATM 24 C C2 SAH . . . B 2 -7.908 10.278 26.198 1 30.81 ? C2 SAH 301 A 1 HETATM 25 N N3 SAH . . . B 2 -6.792 10.479 25.411 1 26.57 ? N3 SAH 301 A 1 HETATM 26 C C4 SAH . . . B 2 -5.642 10.682 26.125 1 30.52 ? C4 SAH 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 685 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 26 #