data_3M53 # _model_server_result.job_id PTqx0uBGYlgsxgPu8SOHFA _model_server_result.datetime_utc '2025-07-03 02:22:53' _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 3m53 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":800}' # _entry.id 3M53 # _exptl.entry_id 3M53 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 3 _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 120 _cell.entry_id 3M53 _cell.length_a 83.746 _cell.length_b 83.746 _cell.length_c 96.111 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3M53 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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 _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id C _struct_conn.ptnr1_label_comp_id ACE _struct_conn.ptnr1_label_seq_id 1 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id ACE _struct_conn.ptnr1_auth_seq_id 185 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id N _struct_conn.ptnr2_label_comp_id SER _struct_conn.ptnr2_label_seq_id 2 _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id SER _struct_conn.ptnr2_auth_seq_id 186 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 1.336 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _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 N CA SAH sing 283 n n N HN1 SAH sing 284 n n N HN2 SAH sing 285 n n CA CB SAH sing 286 n n CA C SAH sing 287 n n CA HA SAH sing 288 n n CB CG SAH sing 289 n n CB HB1 SAH sing 290 n n CB HB2 SAH sing 291 n n CG SD SAH sing 292 n n CG HG1 SAH sing 293 n n CG HG2 SAH sing 294 n n SD C5' SAH sing 295 n n C O SAH doub 296 n n C OXT SAH sing 297 n n OXT HXT SAH sing 298 n n C5' C4' SAH sing 299 n n C5' "H5'1" SAH sing 300 n n C5' "H5'2" SAH sing 301 n n C4' O4' SAH sing 302 n n C4' C3' SAH sing 303 n n C4' H4' SAH sing 304 n n O4' C1' SAH sing 305 n n C3' O3' SAH sing 306 n n C3' C2' SAH sing 307 n n C3' H3' SAH sing 308 n n O3' HO3' SAH sing 309 n n C2' O2' SAH sing 310 n n C2' C1' SAH sing 311 n n C2' H2' SAH sing 312 n n O2' HO2' SAH sing 313 n n C1' N9 SAH sing 314 n n C1' H1' SAH sing 315 n n N9 C8 SAH sing 316 n y N9 C4 SAH sing 317 n y C8 N7 SAH doub 318 n y C8 H8 SAH sing 319 n n N7 C5 SAH sing 320 n y C5 C6 SAH sing 321 n y C5 C4 SAH doub 322 n y C6 N6 SAH sing 323 n n C6 N1 SAH doub 324 n y N6 HN61 SAH sing 325 n n N6 HN62 SAH sing 326 n n N1 C2 SAH sing 327 n y C2 N3 SAH doub 328 n y C2 H2 SAH sing 329 n n N3 C4 SAH sing 330 n y # _atom_sites.entry_id 3M53 _atom_sites.fract_transf_matrix[1][1] 0.011941 _atom_sites.fract_transf_matrix[1][2] 0.006894 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013788 _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] 0.010405 _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 3 SAH A 1 800 800 SAH SAH . D 4 HOH A 1 1 1 HOH HOH . D 4 HOH A 2 3 3 HOH HOH . D 4 HOH A 3 4 4 HOH HOH . D 4 HOH A 4 5 5 HOH HOH . D 4 HOH A 5 6 6 HOH HOH . D 4 HOH A 6 7 7 HOH HOH . D 4 HOH A 7 8 8 HOH HOH . D 4 HOH A 8 9 9 HOH HOH . D 4 HOH A 9 10 10 HOH HOH . D 4 HOH A 10 11 11 HOH HOH . D 4 HOH A 11 12 12 HOH HOH . D 4 HOH A 12 13 13 HOH HOH . D 4 HOH A 13 14 14 HOH HOH . D 4 HOH A 14 15 15 HOH HOH . D 4 HOH A 15 16 16 HOH HOH . D 4 HOH A 16 17 17 HOH HOH . D 4 HOH A 17 18 18 HOH HOH . D 4 HOH A 18 19 19 HOH HOH . D 4 HOH A 19 20 20 HOH HOH . D 4 HOH A 20 21 21 HOH HOH . D 4 HOH A 21 22 22 HOH HOH . D 4 HOH A 22 23 23 HOH HOH . D 4 HOH A 23 24 24 HOH HOH . D 4 HOH A 24 25 25 HOH HOH . D 4 HOH A 25 26 26 HOH HOH . D 4 HOH A 26 27 27 HOH HOH . D 4 HOH A 27 28 28 HOH HOH . D 4 HOH A 28 29 29 HOH HOH . D 4 HOH A 29 30 30 HOH HOH . D 4 HOH A 30 32 32 HOH HOH . D 4 HOH A 31 33 33 HOH HOH . D 4 HOH A 32 34 34 HOH HOH . D 4 HOH A 33 35 35 HOH HOH . D 4 HOH A 34 36 36 HOH HOH . D 4 HOH A 35 37 37 HOH HOH . D 4 HOH A 36 38 38 HOH HOH . D 4 HOH A 37 39 39 HOH HOH . D 4 HOH A 38 40 40 HOH HOH . D 4 HOH A 39 41 41 HOH HOH . D 4 HOH A 40 42 42 HOH HOH . D 4 HOH A 41 43 43 HOH HOH . D 4 HOH A 42 45 45 HOH HOH . D 4 HOH A 43 46 46 HOH HOH . D 4 HOH A 44 47 47 HOH HOH . D 4 HOH A 45 48 48 HOH HOH . D 4 HOH A 46 49 49 HOH HOH . D 4 HOH A 47 50 50 HOH HOH . D 4 HOH A 48 51 51 HOH HOH . D 4 HOH A 49 52 52 HOH HOH . D 4 HOH A 50 53 53 HOH HOH . D 4 HOH A 51 54 54 HOH HOH . D 4 HOH A 52 55 55 HOH HOH . D 4 HOH A 53 56 56 HOH HOH . D 4 HOH A 54 57 57 HOH HOH . D 4 HOH A 55 58 58 HOH HOH . D 4 HOH A 56 59 59 HOH HOH . D 4 HOH A 57 60 60 HOH HOH . D 4 HOH A 58 61 61 HOH HOH . D 4 HOH A 59 62 62 HOH HOH . D 4 HOH A 60 63 63 HOH HOH . D 4 HOH A 61 64 64 HOH HOH . D 4 HOH A 62 65 65 HOH HOH . D 4 HOH A 63 66 66 HOH HOH . D 4 HOH A 64 67 67 HOH HOH . D 4 HOH A 65 68 68 HOH HOH . D 4 HOH A 66 69 69 HOH HOH . D 4 HOH A 67 70 70 HOH HOH . D 4 HOH A 68 72 72 HOH HOH . D 4 HOH A 69 73 73 HOH HOH . D 4 HOH A 70 74 74 HOH HOH . D 4 HOH A 71 75 75 HOH HOH . D 4 HOH A 72 76 76 HOH HOH . D 4 HOH A 73 77 77 HOH HOH . D 4 HOH A 74 78 78 HOH HOH . D 4 HOH A 75 79 79 HOH HOH . D 4 HOH A 76 80 80 HOH HOH . D 4 HOH A 77 81 81 HOH HOH . D 4 HOH A 78 82 82 HOH HOH . D 4 HOH A 79 83 83 HOH HOH . D 4 HOH A 80 84 84 HOH HOH . D 4 HOH A 81 85 85 HOH HOH . D 4 HOH A 82 87 87 HOH HOH . D 4 HOH A 83 88 88 HOH HOH . D 4 HOH A 84 89 89 HOH HOH . D 4 HOH A 85 90 90 HOH HOH . D 4 HOH A 86 91 91 HOH HOH . D 4 HOH A 87 92 92 HOH HOH . D 4 HOH A 88 93 93 HOH HOH . D 4 HOH A 89 94 94 HOH HOH . D 4 HOH A 90 95 95 HOH HOH . D 4 HOH A 91 96 96 HOH HOH . D 4 HOH A 92 97 97 HOH HOH . D 4 HOH A 93 98 98 HOH HOH . D 4 HOH A 94 99 99 HOH HOH . D 4 HOH A 95 100 100 HOH HOH . D 4 HOH A 96 101 101 HOH HOH . D 4 HOH A 97 102 102 HOH HOH . D 4 HOH A 98 103 103 HOH HOH . D 4 HOH A 99 104 104 HOH HOH . D 4 HOH A 100 105 105 HOH HOH . D 4 HOH A 101 367 107 HOH HOH . D 4 HOH A 102 368 109 HOH HOH . D 4 HOH A 103 369 111 HOH HOH . D 4 HOH A 104 370 112 HOH HOH . D 4 HOH A 105 371 113 HOH HOH . D 4 HOH A 106 372 114 HOH HOH . D 4 HOH A 107 373 115 HOH HOH . D 4 HOH A 108 374 116 HOH HOH . D 4 HOH A 109 375 117 HOH HOH . D 4 HOH A 110 376 118 HOH HOH . D 4 HOH A 111 377 119 HOH HOH . D 4 HOH A 112 378 120 HOH HOH . D 4 HOH A 113 379 121 HOH HOH . D 4 HOH A 114 380 122 HOH HOH . D 4 HOH A 115 381 124 HOH HOH . D 4 HOH A 116 382 125 HOH HOH . D 4 HOH A 117 383 126 HOH HOH . D 4 HOH A 118 384 127 HOH HOH . D 4 HOH A 119 385 128 HOH HOH . D 4 HOH A 120 386 129 HOH HOH . D 4 HOH A 121 387 130 HOH HOH . D 4 HOH A 122 388 131 HOH HOH . D 4 HOH A 123 389 132 HOH HOH . D 4 HOH A 124 390 134 HOH HOH . D 4 HOH A 125 391 136 HOH HOH . D 4 HOH A 126 392 137 HOH HOH . D 4 HOH A 127 393 138 HOH HOH . D 4 HOH A 128 394 139 HOH HOH . D 4 HOH A 129 395 140 HOH HOH . D 4 HOH A 130 396 141 HOH HOH . D 4 HOH A 131 397 142 HOH HOH . D 4 HOH A 132 398 143 HOH HOH . D 4 HOH A 133 399 144 HOH HOH . D 4 HOH A 134 400 145 HOH HOH . D 4 HOH A 135 401 146 HOH HOH . D 4 HOH A 136 402 147 HOH HOH . D 4 HOH A 137 403 148 HOH HOH . D 4 HOH A 138 404 149 HOH HOH . D 4 HOH A 139 405 150 HOH HOH . D 4 HOH A 140 406 151 HOH HOH . D 4 HOH A 141 407 152 HOH HOH . D 4 HOH A 142 408 156 HOH HOH . D 4 HOH A 143 409 157 HOH HOH . D 4 HOH A 144 410 158 HOH HOH . D 4 HOH A 145 411 159 HOH HOH . D 4 HOH A 146 412 160 HOH HOH . D 4 HOH A 147 413 161 HOH HOH . D 4 HOH A 148 414 163 HOH HOH . D 4 HOH A 149 415 164 HOH HOH . D 4 HOH A 150 416 165 HOH HOH . D 4 HOH A 151 417 166 HOH HOH . D 4 HOH A 152 418 167 HOH HOH . D 4 HOH A 153 419 168 HOH HOH . D 4 HOH A 154 420 169 HOH HOH . D 4 HOH A 155 421 170 HOH HOH . D 4 HOH A 156 422 171 HOH HOH . D 4 HOH A 157 423 172 HOH HOH . D 4 HOH A 158 424 173 HOH HOH . D 4 HOH A 159 425 174 HOH HOH . D 4 HOH A 160 426 175 HOH HOH . D 4 HOH A 161 427 177 HOH HOH . D 4 HOH A 162 428 178 HOH HOH . D 4 HOH A 163 429 179 HOH HOH . D 4 HOH A 164 430 180 HOH HOH . D 4 HOH A 165 431 182 HOH HOH . D 4 HOH A 166 432 184 HOH HOH . D 4 HOH A 167 433 186 HOH HOH . D 4 HOH A 168 434 187 HOH HOH . D 4 HOH A 169 435 188 HOH HOH . D 4 HOH A 170 436 189 HOH HOH . D 4 HOH A 171 437 190 HOH HOH . D 4 HOH A 172 438 191 HOH HOH . D 4 HOH A 173 439 192 HOH HOH . D 4 HOH A 174 440 193 HOH HOH . D 4 HOH A 175 441 194 HOH HOH . D 4 HOH A 176 442 195 HOH HOH . D 4 HOH A 177 443 197 HOH HOH . D 4 HOH A 178 444 198 HOH HOH . D 4 HOH A 179 445 199 HOH HOH . D 4 HOH A 180 446 200 HOH HOH . D 4 HOH A 181 447 202 HOH HOH . D 4 HOH A 182 448 203 HOH HOH . D 4 HOH A 183 449 204 HOH HOH . D 4 HOH A 184 450 205 HOH HOH . D 4 HOH A 185 451 206 HOH HOH . D 4 HOH A 186 452 207 HOH HOH . D 4 HOH A 187 453 208 HOH HOH . D 4 HOH A 188 454 209 HOH HOH . D 4 HOH A 189 455 211 HOH HOH . D 4 HOH A 190 456 212 HOH HOH . D 4 HOH A 191 457 213 HOH HOH . D 4 HOH A 192 458 214 HOH HOH . D 4 HOH A 193 459 215 HOH HOH . D 4 HOH A 194 460 216 HOH HOH . D 4 HOH A 195 461 217 HOH HOH . D 4 HOH A 196 462 218 HOH HOH . D 4 HOH A 197 463 219 HOH HOH . D 4 HOH A 198 464 220 HOH HOH . D 4 HOH A 199 465 221 HOH HOH . D 4 HOH A 200 466 222 HOH HOH . D 4 HOH A 201 467 224 HOH HOH . D 4 HOH A 202 468 226 HOH HOH . D 4 HOH A 203 469 227 HOH HOH . D 4 HOH A 204 470 228 HOH HOH . E 4 HOH B 1 2 2 HOH HOH . E 4 HOH B 2 44 44 HOH HOH . E 4 HOH B 3 108 108 HOH HOH . E 4 HOH B 4 110 110 HOH HOH . E 4 HOH B 5 155 155 HOH HOH . E 4 HOH B 6 201 201 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 3 -29.511 20.338 -9.47 1 33.03 ? N SAH 800 A 1 HETATM 2 C CA SAH . . . C 3 -30.593 19.49 -10.063 1 33.72 ? CA SAH 800 A 1 HETATM 3 C CB SAH . . . C 3 -31.924 19.927 -9.441 1 33.2 ? CB SAH 800 A 1 HETATM 4 C CG SAH . . . C 3 -32.091 19.237 -8.091 1 32.87 ? CG SAH 800 A 1 HETATM 5 S SD SAH . . . C 3 -32.402 17.501 -8.31 1 36.93 ? SD SAH 800 A 1 HETATM 6 C C SAH . . . C 3 -30.693 19.611 -11.557 1 33.62 ? C SAH 800 A 1 HETATM 7 O O SAH . . . C 3 -31.634 19.057 -12.181 1 33.13 ? O SAH 800 A 1 HETATM 8 O OXT SAH . . . C 3 -29.871 20.286 -12.197 1 33.77 ? OXT SAH 800 A 1 HETATM 9 C C5' SAH . . . C 3 -31.377 16.706 -7.089 1 36.99 ? C5' SAH 800 A 1 HETATM 10 C C4' SAH . . . C 3 -29.926 16.673 -7.558 1 38.63 ? C4' SAH 800 A 1 HETATM 11 O O4' SAH . . . C 3 -29.386 17.985 -7.533 1 36.4 ? O4' SAH 800 A 1 HETATM 12 C C3' SAH . . . C 3 -28.976 15.848 -6.688 1 40.81 ? C3' SAH 800 A 1 HETATM 13 O O3' SAH . . . C 3 -28.824 14.544 -7.235 1 42.01 ? O3' SAH 800 A 1 HETATM 14 C C2' SAH . . . C 3 -27.655 16.605 -6.703 1 40.75 ? C2' SAH 800 A 1 HETATM 15 O O2' SAH . . . C 3 -26.922 16.288 -7.876 1 43.41 ? O2' SAH 800 A 1 HETATM 16 C C1' SAH . . . C 3 -28.075 18.033 -6.935 1 40.44 ? C1' SAH 800 A 1 HETATM 17 N N9 SAH . . . C 3 -28.061 18.787 -5.658 1 41.62 ? N9 SAH 800 A 1 HETATM 18 C C8 SAH . . . C 3 -29.145 19.216 -4.978 1 42.07 ? C8 SAH 800 A 1 HETATM 19 N N7 SAH . . . C 3 -28.795 19.887 -3.853 1 42.22 ? N7 SAH 800 A 1 HETATM 20 C C5 SAH . . . C 3 -27.448 19.89 -3.8 1 44.02 ? C5 SAH 800 A 1 HETATM 21 C C6 SAH . . . C 3 -26.431 20.417 -2.855 1 44.67 ? C6 SAH 800 A 1 HETATM 22 N N6 SAH . . . C 3 -26.82 21.098 -1.745 1 43.57 ? N6 SAH 800 A 1 HETATM 23 N N1 SAH . . . C 3 -25.124 20.191 -3.152 1 44.43 ? N1 SAH 800 A 1 HETATM 24 C C2 SAH . . . C 3 -24.753 19.521 -4.263 1 44.95 ? C2 SAH 800 A 1 HETATM 25 N N3 SAH . . . C 3 -25.625 18.996 -5.154 1 44.06 ? N3 SAH 800 A 1 HETATM 26 C C4 SAH . . . C 3 -26.966 19.151 -4.977 1 43.72 ? C4 SAH 800 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #