data_2P5F # _model_server_result.job_id qXKOJaiMBsCOmtMk7Yx_-A _model_server_result.datetime_utc '2024-11-29 13:20:12' _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 2p5f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 2P5F # _exptl.entry_id 2P5F _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 2P5F _cell.length_a 104.773 _cell.length_b 104.773 _cell.length_c 139.958 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2P5F _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # 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 PQS 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 1 1 A,B,C,D,E 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' 7_466 y-1,x+1,-z+1 0 1 0 1 0 0 0 0 -1 -104.773 104.773 139.958 # _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 '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 2P5F _atom_sites.fract_transf_matrix[1][1] 0.009544 _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] 0.009544 _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] 0.007145 _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 SAH A 1 301 301 SAH SAH . D 3 HOH A 1 302 5 HOH HOH . D 3 HOH A 2 303 7 HOH HOH . D 3 HOH A 3 304 8 HOH HOH . D 3 HOH A 4 305 11 HOH HOH . D 3 HOH A 5 306 13 HOH HOH . D 3 HOH A 6 307 15 HOH HOH . D 3 HOH A 7 308 16 HOH HOH . D 3 HOH A 8 309 19 HOH HOH . D 3 HOH A 9 310 22 HOH HOH . D 3 HOH A 10 311 23 HOH HOH . D 3 HOH A 11 312 24 HOH HOH . D 3 HOH A 12 313 25 HOH HOH . D 3 HOH A 13 314 26 HOH HOH . D 3 HOH A 14 315 27 HOH HOH . D 3 HOH A 15 316 31 HOH HOH . D 3 HOH A 16 317 34 HOH HOH . D 3 HOH A 17 318 38 HOH HOH . D 3 HOH A 18 319 39 HOH HOH . D 3 HOH A 19 320 40 HOH HOH . D 3 HOH A 20 321 42 HOH HOH . D 3 HOH A 21 322 44 HOH HOH . D 3 HOH A 22 323 46 HOH HOH . D 3 HOH A 23 324 49 HOH HOH . D 3 HOH A 24 325 51 HOH HOH . D 3 HOH A 25 326 52 HOH HOH . D 3 HOH A 26 327 54 HOH HOH . D 3 HOH A 27 328 55 HOH HOH . D 3 HOH A 28 329 56 HOH HOH . D 3 HOH A 29 330 59 HOH HOH . D 3 HOH A 30 331 62 HOH HOH . D 3 HOH A 31 332 64 HOH HOH . D 3 HOH A 32 333 70 HOH HOH . D 3 HOH A 33 334 71 HOH HOH . D 3 HOH A 34 335 73 HOH HOH . D 3 HOH A 35 336 76 HOH HOH . D 3 HOH A 36 337 77 HOH HOH . D 3 HOH A 37 338 78 HOH HOH . D 3 HOH A 38 339 79 HOH HOH . D 3 HOH A 39 340 82 HOH HOH . D 3 HOH A 40 341 90 HOH HOH . D 3 HOH A 41 342 91 HOH HOH . D 3 HOH A 42 343 93 HOH HOH . D 3 HOH A 43 344 95 HOH HOH . D 3 HOH A 44 345 96 HOH HOH . D 3 HOH A 45 346 99 HOH HOH . D 3 HOH A 46 347 100 HOH HOH . D 3 HOH A 47 348 103 HOH HOH . D 3 HOH A 48 349 104 HOH HOH . D 3 HOH A 49 350 107 HOH HOH . D 3 HOH A 50 351 108 HOH HOH . D 3 HOH A 51 352 114 HOH HOH . D 3 HOH A 52 353 116 HOH HOH . D 3 HOH A 53 354 117 HOH HOH . D 3 HOH A 54 355 118 HOH HOH . D 3 HOH A 55 356 119 HOH HOH . D 3 HOH A 56 357 122 HOH HOH . D 3 HOH A 57 358 124 HOH HOH . D 3 HOH A 58 359 125 HOH HOH . D 3 HOH A 59 360 126 HOH HOH . D 3 HOH A 60 361 127 HOH HOH . D 3 HOH A 61 362 129 HOH HOH . D 3 HOH A 62 363 130 HOH HOH . D 3 HOH A 63 364 134 HOH HOH . D 3 HOH A 64 365 137 HOH HOH . D 3 HOH A 65 366 140 HOH HOH . D 3 HOH A 66 367 146 HOH HOH . D 3 HOH A 67 368 149 HOH HOH . D 3 HOH A 68 369 155 HOH HOH . D 3 HOH A 69 370 159 HOH HOH . D 3 HOH A 70 371 160 HOH HOH . D 3 HOH A 71 372 161 HOH HOH . D 3 HOH A 72 373 162 HOH HOH . D 3 HOH A 73 374 163 HOH HOH . D 3 HOH A 74 375 166 HOH HOH . D 3 HOH A 75 376 169 HOH HOH . D 3 HOH A 76 377 170 HOH HOH . D 3 HOH A 77 378 171 HOH HOH . D 3 HOH A 78 379 172 HOH HOH . D 3 HOH A 79 380 176 HOH HOH . D 3 HOH A 80 381 179 HOH HOH . D 3 HOH A 81 382 181 HOH HOH . D 3 HOH A 82 383 182 HOH HOH . D 3 HOH A 83 384 184 HOH HOH . D 3 HOH A 84 385 185 HOH HOH . D 3 HOH A 85 386 186 HOH HOH . D 3 HOH A 86 387 189 HOH HOH . D 3 HOH A 87 388 191 HOH HOH . D 3 HOH A 88 389 193 HOH HOH . D 3 HOH A 89 390 194 HOH HOH . D 3 HOH A 90 391 195 HOH HOH . D 3 HOH A 91 392 196 HOH HOH . D 3 HOH A 92 393 197 HOH HOH . D 3 HOH A 93 394 198 HOH HOH . D 3 HOH A 94 395 202 HOH HOH . D 3 HOH A 95 396 204 HOH HOH . D 3 HOH A 96 397 209 HOH HOH . D 3 HOH A 97 398 215 HOH HOH . D 3 HOH A 98 399 217 HOH HOH . D 3 HOH A 99 400 218 HOH HOH . D 3 HOH A 100 401 221 HOH HOH . D 3 HOH A 101 402 222 HOH HOH . D 3 HOH A 102 403 223 HOH HOH . D 3 HOH A 103 404 226 HOH HOH . D 3 HOH A 104 405 231 HOH HOH . D 3 HOH A 105 406 232 HOH HOH . D 3 HOH A 106 407 233 HOH HOH . E 3 HOH B 1 266 1 HOH HOH . E 3 HOH B 2 267 2 HOH HOH . E 3 HOH B 3 268 3 HOH HOH . E 3 HOH B 4 269 4 HOH HOH . E 3 HOH B 5 270 6 HOH HOH . E 3 HOH B 6 271 9 HOH HOH . E 3 HOH B 7 272 10 HOH HOH . E 3 HOH B 8 273 12 HOH HOH . E 3 HOH B 9 274 14 HOH HOH . E 3 HOH B 10 275 17 HOH HOH . E 3 HOH B 11 276 18 HOH HOH . E 3 HOH B 12 277 20 HOH HOH . E 3 HOH B 13 278 21 HOH HOH . E 3 HOH B 14 279 28 HOH HOH . E 3 HOH B 15 280 29 HOH HOH . E 3 HOH B 16 281 30 HOH HOH . E 3 HOH B 17 282 32 HOH HOH . E 3 HOH B 18 283 33 HOH HOH . E 3 HOH B 19 284 35 HOH HOH . E 3 HOH B 20 285 36 HOH HOH . E 3 HOH B 21 286 37 HOH HOH . E 3 HOH B 22 287 41 HOH HOH . E 3 HOH B 23 288 43 HOH HOH . E 3 HOH B 24 289 45 HOH HOH . E 3 HOH B 25 290 47 HOH HOH . E 3 HOH B 26 291 48 HOH HOH . E 3 HOH B 27 292 50 HOH HOH . E 3 HOH B 28 293 53 HOH HOH . E 3 HOH B 29 294 57 HOH HOH . E 3 HOH B 30 295 58 HOH HOH . E 3 HOH B 31 296 60 HOH HOH . E 3 HOH B 32 297 61 HOH HOH . E 3 HOH B 33 298 63 HOH HOH . E 3 HOH B 34 299 65 HOH HOH . E 3 HOH B 35 300 66 HOH HOH . E 3 HOH B 36 301 67 HOH HOH . E 3 HOH B 37 302 68 HOH HOH . E 3 HOH B 38 303 69 HOH HOH . E 3 HOH B 39 304 72 HOH HOH . E 3 HOH B 40 305 74 HOH HOH . E 3 HOH B 41 306 75 HOH HOH . E 3 HOH B 42 307 80 HOH HOH . E 3 HOH B 43 308 81 HOH HOH . E 3 HOH B 44 309 83 HOH HOH . E 3 HOH B 45 310 84 HOH HOH . E 3 HOH B 46 311 85 HOH HOH . E 3 HOH B 47 312 86 HOH HOH . E 3 HOH B 48 313 87 HOH HOH . E 3 HOH B 49 314 88 HOH HOH . E 3 HOH B 50 315 89 HOH HOH . E 3 HOH B 51 316 92 HOH HOH . E 3 HOH B 52 317 94 HOH HOH . E 3 HOH B 53 318 97 HOH HOH . E 3 HOH B 54 319 98 HOH HOH . E 3 HOH B 55 320 101 HOH HOH . E 3 HOH B 56 321 102 HOH HOH . E 3 HOH B 57 322 105 HOH HOH . E 3 HOH B 58 323 106 HOH HOH . E 3 HOH B 59 324 109 HOH HOH . E 3 HOH B 60 325 110 HOH HOH . E 3 HOH B 61 326 111 HOH HOH . E 3 HOH B 62 327 112 HOH HOH . E 3 HOH B 63 328 113 HOH HOH . E 3 HOH B 64 329 115 HOH HOH . E 3 HOH B 65 330 120 HOH HOH . E 3 HOH B 66 331 121 HOH HOH . E 3 HOH B 67 332 123 HOH HOH . E 3 HOH B 68 333 128 HOH HOH . E 3 HOH B 69 334 131 HOH HOH . E 3 HOH B 70 335 132 HOH HOH . E 3 HOH B 71 336 133 HOH HOH . E 3 HOH B 72 337 135 HOH HOH . E 3 HOH B 73 338 136 HOH HOH . E 3 HOH B 74 339 138 HOH HOH . E 3 HOH B 75 340 139 HOH HOH . E 3 HOH B 76 341 141 HOH HOH . E 3 HOH B 77 342 142 HOH HOH . E 3 HOH B 78 343 143 HOH HOH . E 3 HOH B 79 344 144 HOH HOH . E 3 HOH B 80 345 145 HOH HOH . E 3 HOH B 81 346 147 HOH HOH . E 3 HOH B 82 347 148 HOH HOH . E 3 HOH B 83 348 150 HOH HOH . E 3 HOH B 84 349 151 HOH HOH . E 3 HOH B 85 350 152 HOH HOH . E 3 HOH B 86 351 153 HOH HOH . E 3 HOH B 87 352 154 HOH HOH . E 3 HOH B 88 353 156 HOH HOH . E 3 HOH B 89 354 157 HOH HOH . E 3 HOH B 90 355 158 HOH HOH . E 3 HOH B 91 356 164 HOH HOH . E 3 HOH B 92 357 165 HOH HOH . E 3 HOH B 93 358 167 HOH HOH . E 3 HOH B 94 359 168 HOH HOH . E 3 HOH B 95 360 173 HOH HOH . E 3 HOH B 96 361 174 HOH HOH . E 3 HOH B 97 362 175 HOH HOH . E 3 HOH B 98 363 177 HOH HOH . E 3 HOH B 99 364 178 HOH HOH . E 3 HOH B 100 365 180 HOH HOH . E 3 HOH B 101 366 183 HOH HOH . E 3 HOH B 102 367 187 HOH HOH . E 3 HOH B 103 368 188 HOH HOH . E 3 HOH B 104 369 190 HOH HOH . E 3 HOH B 105 370 192 HOH HOH . E 3 HOH B 106 371 199 HOH HOH . E 3 HOH B 107 372 200 HOH HOH . E 3 HOH B 108 373 201 HOH HOH . E 3 HOH B 109 374 203 HOH HOH . E 3 HOH B 110 375 205 HOH HOH . E 3 HOH B 111 376 206 HOH HOH . E 3 HOH B 112 377 207 HOH HOH . E 3 HOH B 113 378 208 HOH HOH . E 3 HOH B 114 379 210 HOH HOH . E 3 HOH B 115 380 211 HOH HOH . E 3 HOH B 116 381 212 HOH HOH . E 3 HOH B 117 382 213 HOH HOH . E 3 HOH B 118 383 214 HOH HOH . E 3 HOH B 119 384 216 HOH HOH . E 3 HOH B 120 385 219 HOH HOH . E 3 HOH B 121 386 220 HOH HOH . E 3 HOH B 122 387 224 HOH HOH . E 3 HOH B 123 388 225 HOH HOH . E 3 HOH B 124 389 227 HOH HOH . E 3 HOH B 125 390 228 HOH HOH . E 3 HOH B 126 391 229 HOH HOH . E 3 HOH B 127 392 230 HOH HOH . E 3 HOH B 128 393 234 HOH HOH . E 3 HOH B 129 394 235 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 . . . C 2 33.546 92.585 67.438 1 37.48 ? N SAH 301 A 1 HETATM 2 C CA SAH . . . C 2 32.101 92.112 67.335 1 38.41 ? CA SAH 301 A 1 HETATM 3 C CB SAH . . . C 2 31.483 91.449 68.543 1 38.87 ? CB SAH 301 A 1 HETATM 4 C CG SAH . . . C 2 32.123 90.207 69.139 1 40.39 ? CG SAH 301 A 1 HETATM 5 S SD SAH . . . C 2 30.923 89.473 70.345 1 42.46 ? SD SAH 301 A 1 HETATM 6 C C SAH . . . C 2 31.259 93.386 66.903 1 38.03 ? C SAH 301 A 1 HETATM 7 O O SAH . . . C 2 31.849 94.47 66.742 1 37.31 ? O SAH 301 A 1 HETATM 8 O OXT SAH . . . C 2 29.991 93.21 66.744 1 39.02 ? OXT SAH 301 A 1 HETATM 9 C C5' SAH . . . C 2 30.042 88.306 69.392 1 39.22 ? C5' SAH 301 A 1 HETATM 10 C C4' SAH . . . C 2 28.55 88.294 69.906 1 38.14 ? C4' SAH 301 A 1 HETATM 11 O O4' SAH . . . C 2 27.979 89.604 69.645 1 37.82 ? O4' SAH 301 A 1 HETATM 12 C C3' SAH . . . C 2 27.65 87.301 69.261 1 37.17 ? C3' SAH 301 A 1 HETATM 13 O O3' SAH . . . C 2 27.747 86.032 69.893 1 38.83 ? O3' SAH 301 A 1 HETATM 14 C C2' SAH . . . C 2 26.268 87.996 69.392 1 36.91 ? C2' SAH 301 A 1 HETATM 15 O O2' SAH . . . C 2 25.629 87.768 70.651 1 34.85 ? O2' SAH 301 A 1 HETATM 16 C C1' SAH . . . C 2 26.58 89.502 69.088 1 35.79 ? C1' SAH 301 A 1 HETATM 17 N N9 SAH . . . C 2 26.514 89.889 67.727 1 34.87 ? N9 SAH 301 A 1 HETATM 18 C C8 SAH . . . C 2 27.472 90.153 66.761 1 35.48 ? C8 SAH 301 A 1 HETATM 19 N N7 SAH . . . C 2 26.999 90.486 65.588 1 35.56 ? N7 SAH 301 A 1 HETATM 20 C C5 SAH . . . C 2 25.588 90.454 65.751 1 34.17 ? C5 SAH 301 A 1 HETATM 21 C C6 SAH . . . C 2 24.509 90.728 64.831 1 35.87 ? C6 SAH 301 A 1 HETATM 22 N N6 SAH . . . C 2 24.685 91.09 63.557 1 37.67 ? N6 SAH 301 A 1 HETATM 23 N N1 SAH . . . C 2 23.243 90.587 65.359 1 36.5 ? N1 SAH 301 A 1 HETATM 24 C C2 SAH . . . C 2 23.009 90.219 66.655 1 36.5 ? C2 SAH 301 A 1 HETATM 25 N N3 SAH . . . C 2 24.012 89.953 67.562 1 35.01 ? N3 SAH 301 A 1 HETATM 26 C C4 SAH . . . C 2 25.271 90.09 67.041 1 34.83 ? C4 SAH 301 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 443 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 26 #