data_3NDC # _model_server_result.job_id c46nFa1v7Sqy8YZfpNb3dw _model_server_result.datetime_utc '2024-10-25 20:23:19' _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 3ndc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":300}' # _entry.id 3NDC # _exptl.entry_id 3NDC _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 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 120 _cell.entry_id 3NDC _cell.length_a 84.517 _cell.length_b 84.517 _cell.length_c 144.637 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NDC _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N 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 3NDC _atom_sites.fract_transf_matrix[1][1] 0.011832 _atom_sites.fract_transf_matrix[1][2] 0.006831 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013662 _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] 0.006914 _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 1 300 300 SAH SAH . D 2 SAH B 1 300 300 SAH SAH . E 3 HOH A 1 262 1 HOH HOH . E 3 HOH A 2 263 3 HOH HOH . E 3 HOH A 3 264 4 HOH HOH . E 3 HOH A 4 265 7 HOH HOH . E 3 HOH A 5 266 8 HOH HOH . E 3 HOH A 6 267 9 HOH HOH . E 3 HOH A 7 268 12 HOH HOH . E 3 HOH A 8 269 13 HOH HOH . E 3 HOH A 9 270 15 HOH HOH . E 3 HOH A 10 271 20 HOH HOH . E 3 HOH A 11 272 23 HOH HOH . E 3 HOH A 12 273 25 HOH HOH . E 3 HOH A 13 274 29 HOH HOH . E 3 HOH A 14 275 30 HOH HOH . E 3 HOH A 15 276 31 HOH HOH . E 3 HOH A 16 277 33 HOH HOH . E 3 HOH A 17 278 34 HOH HOH . E 3 HOH A 18 279 35 HOH HOH . E 3 HOH A 19 280 36 HOH HOH . E 3 HOH A 20 281 37 HOH HOH . E 3 HOH A 21 282 38 HOH HOH . E 3 HOH A 22 283 39 HOH HOH . E 3 HOH A 23 284 42 HOH HOH . E 3 HOH A 24 285 43 HOH HOH . E 3 HOH A 25 286 44 HOH HOH . E 3 HOH A 26 287 46 HOH HOH . E 3 HOH A 27 288 47 HOH HOH . E 3 HOH A 28 289 49 HOH HOH . E 3 HOH A 29 290 50 HOH HOH . E 3 HOH A 30 291 53 HOH HOH . E 3 HOH A 31 292 54 HOH HOH . E 3 HOH A 32 293 56 HOH HOH . E 3 HOH A 33 294 57 HOH HOH . E 3 HOH A 34 295 59 HOH HOH . E 3 HOH A 35 296 60 HOH HOH . E 3 HOH A 36 297 61 HOH HOH . E 3 HOH A 37 298 62 HOH HOH . E 3 HOH A 38 299 63 HOH HOH . E 3 HOH A 39 301 64 HOH HOH . E 3 HOH A 40 302 65 HOH HOH . E 3 HOH A 41 303 69 HOH HOH . E 3 HOH A 42 304 70 HOH HOH . E 3 HOH A 43 305 73 HOH HOH . E 3 HOH A 44 306 74 HOH HOH . E 3 HOH A 45 307 76 HOH HOH . E 3 HOH A 46 308 77 HOH HOH . E 3 HOH A 47 309 78 HOH HOH . E 3 HOH A 48 310 79 HOH HOH . E 3 HOH A 49 311 80 HOH HOH . E 3 HOH A 50 312 81 HOH HOH . E 3 HOH A 51 313 82 HOH HOH . E 3 HOH A 52 314 83 HOH HOH . E 3 HOH A 53 315 84 HOH HOH . E 3 HOH A 54 316 85 HOH HOH . E 3 HOH A 55 317 88 HOH HOH . E 3 HOH A 56 318 89 HOH HOH . E 3 HOH A 57 319 91 HOH HOH . E 3 HOH A 58 320 92 HOH HOH . E 3 HOH A 59 321 93 HOH HOH . E 3 HOH A 60 322 95 HOH HOH . E 3 HOH A 61 323 96 HOH HOH . E 3 HOH A 62 324 97 HOH HOH . E 3 HOH A 63 325 99 HOH HOH . E 3 HOH A 64 326 102 HOH HOH . E 3 HOH A 65 327 103 HOH HOH . E 3 HOH A 66 328 104 HOH HOH . E 3 HOH A 67 329 106 HOH HOH . E 3 HOH A 68 330 108 HOH HOH . E 3 HOH A 69 331 110 HOH HOH . E 3 HOH A 70 332 111 HOH HOH . E 3 HOH A 71 333 112 HOH HOH . E 3 HOH A 72 334 113 HOH HOH . E 3 HOH A 73 335 118 HOH HOH . E 3 HOH A 74 336 119 HOH HOH . E 3 HOH A 75 337 121 HOH HOH . E 3 HOH A 76 338 123 HOH HOH . E 3 HOH A 77 339 125 HOH HOH . E 3 HOH A 78 340 128 HOH HOH . E 3 HOH A 79 341 131 HOH HOH . E 3 HOH A 80 342 133 HOH HOH . E 3 HOH A 81 343 134 HOH HOH . E 3 HOH A 82 344 138 HOH HOH . E 3 HOH A 83 345 139 HOH HOH . E 3 HOH A 84 346 141 HOH HOH . E 3 HOH A 85 347 142 HOH HOH . E 3 HOH A 86 348 144 HOH HOH . E 3 HOH A 87 349 145 HOH HOH . E 3 HOH A 88 350 150 HOH HOH . E 3 HOH A 89 351 152 HOH HOH . E 3 HOH A 90 352 153 HOH HOH . E 3 HOH A 91 353 158 HOH HOH . E 3 HOH A 92 354 160 HOH HOH . E 3 HOH A 93 355 161 HOH HOH . E 3 HOH A 94 356 162 HOH HOH . E 3 HOH A 95 357 163 HOH HOH . E 3 HOH A 96 358 164 HOH HOH . E 3 HOH A 97 359 169 HOH HOH . E 3 HOH A 98 360 171 HOH HOH . E 3 HOH A 99 361 172 HOH HOH . E 3 HOH A 100 362 173 HOH HOH . E 3 HOH A 101 363 176 HOH HOH . E 3 HOH A 102 364 177 HOH HOH . E 3 HOH A 103 365 178 HOH HOH . E 3 HOH A 104 366 179 HOH HOH . E 3 HOH A 105 367 180 HOH HOH . E 3 HOH A 106 368 181 HOH HOH . E 3 HOH A 107 369 182 HOH HOH . E 3 HOH A 108 370 183 HOH HOH . E 3 HOH A 109 371 184 HOH HOH . E 3 HOH A 110 372 185 HOH HOH . E 3 HOH A 111 373 186 HOH HOH . E 3 HOH A 112 374 187 HOH HOH . E 3 HOH A 113 375 192 HOH HOH . E 3 HOH A 114 376 193 HOH HOH . E 3 HOH A 115 377 195 HOH HOH . E 3 HOH A 116 378 197 HOH HOH . E 3 HOH A 117 379 200 HOH HOH . E 3 HOH A 118 380 203 HOH HOH . E 3 HOH A 119 381 204 HOH HOH . E 3 HOH A 120 382 205 HOH HOH . E 3 HOH A 121 383 208 HOH HOH . E 3 HOH A 122 384 211 HOH HOH . E 3 HOH A 123 385 212 HOH HOH . E 3 HOH A 124 386 213 HOH HOH . E 3 HOH A 125 387 214 HOH HOH . E 3 HOH A 126 388 215 HOH HOH . E 3 HOH A 127 389 216 HOH HOH . E 3 HOH A 128 390 218 HOH HOH . E 3 HOH A 129 391 219 HOH HOH . F 3 HOH B 1 262 2 HOH HOH . F 3 HOH B 2 263 5 HOH HOH . F 3 HOH B 3 264 6 HOH HOH . F 3 HOH B 4 265 10 HOH HOH . F 3 HOH B 5 266 11 HOH HOH . F 3 HOH B 6 267 14 HOH HOH . F 3 HOH B 7 268 16 HOH HOH . F 3 HOH B 8 269 17 HOH HOH . F 3 HOH B 9 270 18 HOH HOH . F 3 HOH B 10 271 19 HOH HOH . F 3 HOH B 11 272 21 HOH HOH . F 3 HOH B 12 273 22 HOH HOH . F 3 HOH B 13 274 24 HOH HOH . F 3 HOH B 14 275 26 HOH HOH . F 3 HOH B 15 276 27 HOH HOH . F 3 HOH B 16 277 28 HOH HOH . F 3 HOH B 17 278 32 HOH HOH . F 3 HOH B 18 279 40 HOH HOH . F 3 HOH B 19 280 41 HOH HOH . F 3 HOH B 20 281 45 HOH HOH . F 3 HOH B 21 282 48 HOH HOH . F 3 HOH B 22 283 51 HOH HOH . F 3 HOH B 23 284 52 HOH HOH . F 3 HOH B 24 285 55 HOH HOH . F 3 HOH B 25 286 58 HOH HOH . F 3 HOH B 26 287 66 HOH HOH . F 3 HOH B 27 288 67 HOH HOH . F 3 HOH B 28 289 68 HOH HOH . F 3 HOH B 29 290 71 HOH HOH . F 3 HOH B 30 291 72 HOH HOH . F 3 HOH B 31 292 75 HOH HOH . F 3 HOH B 32 293 86 HOH HOH . F 3 HOH B 33 294 87 HOH HOH . F 3 HOH B 34 295 90 HOH HOH . F 3 HOH B 35 296 94 HOH HOH . F 3 HOH B 36 297 98 HOH HOH . F 3 HOH B 37 298 100 HOH HOH . F 3 HOH B 38 299 101 HOH HOH . F 3 HOH B 39 301 105 HOH HOH . F 3 HOH B 40 302 107 HOH HOH . F 3 HOH B 41 303 109 HOH HOH . F 3 HOH B 42 304 114 HOH HOH . F 3 HOH B 43 305 115 HOH HOH . F 3 HOH B 44 306 116 HOH HOH . F 3 HOH B 45 307 117 HOH HOH . F 3 HOH B 46 308 120 HOH HOH . F 3 HOH B 47 309 122 HOH HOH . F 3 HOH B 48 310 124 HOH HOH . F 3 HOH B 49 311 126 HOH HOH . F 3 HOH B 50 312 127 HOH HOH . F 3 HOH B 51 313 129 HOH HOH . F 3 HOH B 52 314 130 HOH HOH . F 3 HOH B 53 315 132 HOH HOH . F 3 HOH B 54 316 135 HOH HOH . F 3 HOH B 55 317 136 HOH HOH . F 3 HOH B 56 318 137 HOH HOH . F 3 HOH B 57 319 140 HOH HOH . F 3 HOH B 58 320 143 HOH HOH . F 3 HOH B 59 321 146 HOH HOH . F 3 HOH B 60 322 147 HOH HOH . F 3 HOH B 61 323 148 HOH HOH . F 3 HOH B 62 324 149 HOH HOH . F 3 HOH B 63 325 151 HOH HOH . F 3 HOH B 64 326 154 HOH HOH . F 3 HOH B 65 327 155 HOH HOH . F 3 HOH B 66 328 156 HOH HOH . F 3 HOH B 67 329 157 HOH HOH . F 3 HOH B 68 330 159 HOH HOH . F 3 HOH B 69 331 165 HOH HOH . F 3 HOH B 70 332 166 HOH HOH . F 3 HOH B 71 333 167 HOH HOH . F 3 HOH B 72 334 168 HOH HOH . F 3 HOH B 73 335 170 HOH HOH . F 3 HOH B 74 336 174 HOH HOH . F 3 HOH B 75 337 175 HOH HOH . F 3 HOH B 76 338 188 HOH HOH . F 3 HOH B 77 339 189 HOH HOH . F 3 HOH B 78 340 190 HOH HOH . F 3 HOH B 79 341 191 HOH HOH . F 3 HOH B 80 342 194 HOH HOH . F 3 HOH B 81 343 196 HOH HOH . F 3 HOH B 82 344 198 HOH HOH . F 3 HOH B 83 345 199 HOH HOH . F 3 HOH B 84 346 201 HOH HOH . F 3 HOH B 85 347 202 HOH HOH . F 3 HOH B 86 348 206 HOH HOH . F 3 HOH B 87 349 207 HOH HOH . F 3 HOH B 88 350 209 HOH HOH . F 3 HOH B 89 351 210 HOH HOH . F 3 HOH B 90 352 217 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 35.184 -32.021 3.362 1 25.24 ? N SAH 300 A 1 HETATM 2 C CA SAH . . . C 2 35.44 -32.05 1.899 1 25.09 ? CA SAH 300 A 1 HETATM 3 C CB SAH . . . C 2 36.673 -32.926 1.59 1 23.99 ? CB SAH 300 A 1 HETATM 4 C CG SAH . . . C 2 38.008 -32.37 2.153 1 25.65 ? CG SAH 300 A 1 HETATM 5 S SD SAH . . . C 2 39.328 -33.475 1.728 1 25.97 ? SD SAH 300 A 1 HETATM 6 C C SAH . . . C 2 34.176 -32.544 1.228 1 25.27 ? C SAH 300 A 1 HETATM 7 O O SAH . . . C 2 33.097 -32.54 1.829 1 25.66 ? O SAH 300 A 1 HETATM 8 O OXT SAH . . . C 2 34.166 -32.966 0.06 1 25.12 ? OXT SAH 300 A 1 HETATM 9 C C5' SAH . . . C 2 39.898 -32.724 0.212 1 25 ? C5' SAH 300 A 1 HETATM 10 C C4' SAH . . . C 2 39.551 -33.595 -1.006 1 24.81 ? C4' SAH 300 A 1 HETATM 11 O O4' SAH . . . C 2 38.181 -33.442 -1.441 1 22.72 ? O4' SAH 300 A 1 HETATM 12 C C3' SAH . . . C 2 40.384 -33.257 -2.242 1 24.48 ? C3' SAH 300 A 1 HETATM 13 O O3' SAH . . . C 2 41.636 -33.947 -2.244 1 25.8 ? O3' SAH 300 A 1 HETATM 14 C C2' SAH . . . C 2 39.509 -33.696 -3.384 1 24.12 ? C2' SAH 300 A 1 HETATM 15 O O2' SAH . . . C 2 39.579 -35.123 -3.591 1 26.76 ? O2' SAH 300 A 1 HETATM 16 C C1' SAH . . . C 2 38.121 -33.411 -2.862 1 24.12 ? C1' SAH 300 A 1 HETATM 17 N N9 SAH . . . C 2 37.6 -32.078 -3.27 1 25.48 ? N9 SAH 300 A 1 HETATM 18 C C8 SAH . . . C 2 37.385 -31.041 -2.418 1 24.22 ? C8 SAH 300 A 1 HETATM 19 N N7 SAH . . . C 2 36.838 -29.992 -3.086 1 26 ? N7 SAH 300 A 1 HETATM 20 C C5 SAH . . . C 2 36.722 -30.372 -4.384 1 24.45 ? C5 SAH 300 A 1 HETATM 21 C C6 SAH . . . C 2 36.218 -29.745 -5.615 1 23.1 ? C6 SAH 300 A 1 HETATM 22 N N6 SAH . . . C 2 35.708 -28.494 -5.56 1 23.02 ? N6 SAH 300 A 1 HETATM 23 N N1 SAH . . . C 2 36.25 -30.479 -6.76 1 26.09 ? N1 SAH 300 A 1 HETATM 24 C C2 SAH . . . C 2 36.708 -31.75 -6.799 1 25.2 ? C2 SAH 300 A 1 HETATM 25 N N3 SAH . . . C 2 37.179 -32.39 -5.71 1 25.13 ? N3 SAH 300 A 1 HETATM 26 C C4 SAH . . . C 2 37.218 -31.747 -4.502 1 24.54 ? C4 SAH 300 A 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #