data_3LBY # _model_server_result.job_id tElLkwKTFnixLj4807XnTQ _model_server_result.datetime_utc '2025-07-03 23:13:52' _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 3lby # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":4630}' # _entry.id 3LBY # _exptl.entry_id 3LBY _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 120 _cell.entry_id 3LBY _cell.length_a 92.21 _cell.length_b 92.21 _cell.length_c 107.01 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LBY _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 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 264 n n N HN1 SAH sing 265 n n N HN2 SAH sing 266 n n CA CB SAH sing 267 n n CA C SAH sing 268 n n CA HA SAH sing 269 n n CB CG SAH sing 270 n n CB HB1 SAH sing 271 n n CB HB2 SAH sing 272 n n CG SD SAH sing 273 n n CG HG1 SAH sing 274 n n CG HG2 SAH sing 275 n n SD C5' SAH sing 276 n n C O SAH doub 277 n n C OXT SAH sing 278 n n OXT HXT SAH sing 279 n n C5' C4' SAH sing 280 n n C5' "H5'1" SAH sing 281 n n C5' "H5'2" SAH sing 282 n n C4' O4' SAH sing 283 n n C4' C3' SAH sing 284 n n C4' H4' SAH sing 285 n n O4' C1' SAH sing 286 n n C3' O3' SAH sing 287 n n C3' C2' SAH sing 288 n n C3' H3' SAH sing 289 n n O3' HO3' SAH sing 290 n n C2' O2' SAH sing 291 n n C2' C1' SAH sing 292 n n C2' H2' SAH sing 293 n n O2' HO2' SAH sing 294 n n C1' N9 SAH sing 295 n n C1' H1' SAH sing 296 n n N9 C8 SAH sing 297 n y N9 C4 SAH sing 298 n y C8 N7 SAH doub 299 n y C8 H8 SAH sing 300 n n N7 C5 SAH sing 301 n y C5 C6 SAH sing 302 n y C5 C4 SAH doub 303 n y C6 N6 SAH sing 304 n n C6 N1 SAH doub 305 n y N6 HN61 SAH sing 306 n n N6 HN62 SAH sing 307 n n N1 C2 SAH sing 308 n y C2 N3 SAH doub 309 n y C2 H2 SAH sing 310 n n N3 C4 SAH sing 311 n y # _atom_sites.entry_id 3LBY _atom_sites.fract_transf_matrix[1][1] 0.010845 _atom_sites.fract_transf_matrix[1][2] 0.006261 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012523 _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] 0.009345 _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 4630 4630 SAH SAH . D 3 HOH A 1 182 1 HOH HOH . D 3 HOH A 2 183 2 HOH HOH . D 3 HOH A 3 184 3 HOH HOH . D 3 HOH A 4 185 5 HOH HOH . D 3 HOH A 5 186 6 HOH HOH . D 3 HOH A 6 187 187 HOH HOH . D 3 HOH A 7 188 7 HOH HOH . D 3 HOH A 8 189 189 HOH HOH . D 3 HOH A 9 190 190 HOH HOH . D 3 HOH A 10 191 8 HOH HOH . D 3 HOH A 11 192 10 HOH HOH . D 3 HOH A 12 193 193 HOH HOH . D 3 HOH A 13 194 194 HOH HOH . D 3 HOH A 14 195 195 HOH HOH . D 3 HOH A 15 196 196 HOH HOH . D 3 HOH A 16 197 197 HOH HOH . D 3 HOH A 17 198 198 HOH HOH . D 3 HOH A 18 199 11 HOH HOH . D 3 HOH A 19 200 200 HOH HOH . D 3 HOH A 20 201 12 HOH HOH . D 3 HOH A 21 202 202 HOH HOH . D 3 HOH A 22 203 203 HOH HOH . D 3 HOH A 23 204 13 HOH HOH . D 3 HOH A 24 205 205 HOH HOH . D 3 HOH A 25 206 206 HOH HOH . D 3 HOH A 26 207 207 HOH HOH . D 3 HOH A 27 208 208 HOH HOH . D 3 HOH A 28 209 209 HOH HOH . D 3 HOH A 29 210 14 HOH HOH . D 3 HOH A 30 211 211 HOH HOH . D 3 HOH A 31 212 15 HOH HOH . D 3 HOH A 32 213 17 HOH HOH . D 3 HOH A 33 214 18 HOH HOH . D 3 HOH A 34 215 20 HOH HOH . D 3 HOH A 35 216 21 HOH HOH . D 3 HOH A 36 217 217 HOH HOH . D 3 HOH A 37 218 22 HOH HOH . D 3 HOH A 38 219 23 HOH HOH . D 3 HOH A 39 220 220 HOH HOH . D 3 HOH A 40 221 221 HOH HOH . D 3 HOH A 41 222 24 HOH HOH . D 3 HOH A 42 223 25 HOH HOH . D 3 HOH A 43 224 224 HOH HOH . D 3 HOH A 44 225 225 HOH HOH . D 3 HOH A 45 226 26 HOH HOH . D 3 HOH A 46 227 227 HOH HOH . D 3 HOH A 47 228 228 HOH HOH . D 3 HOH A 48 229 229 HOH HOH . D 3 HOH A 49 230 27 HOH HOH . D 3 HOH A 50 231 231 HOH HOH . D 3 HOH A 51 232 28 HOH HOH . D 3 HOH A 52 233 233 HOH HOH . D 3 HOH A 53 234 234 HOH HOH . D 3 HOH A 54 235 29 HOH HOH . D 3 HOH A 55 236 236 HOH HOH . D 3 HOH A 56 237 31 HOH HOH . D 3 HOH A 57 238 33 HOH HOH . D 3 HOH A 58 239 34 HOH HOH . D 3 HOH A 59 240 35 HOH HOH . D 3 HOH A 60 241 37 HOH HOH . D 3 HOH A 61 242 38 HOH HOH . D 3 HOH A 62 243 243 HOH HOH . D 3 HOH A 63 244 244 HOH HOH . D 3 HOH A 64 245 39 HOH HOH . D 3 HOH A 65 246 40 HOH HOH . D 3 HOH A 66 247 247 HOH HOH . D 3 HOH A 67 248 42 HOH HOH . D 3 HOH A 68 249 44 HOH HOH . D 3 HOH A 69 250 250 HOH HOH . D 3 HOH A 70 251 47 HOH HOH . D 3 HOH A 71 252 252 HOH HOH . D 3 HOH A 72 253 253 HOH HOH . D 3 HOH A 73 254 48 HOH HOH . D 3 HOH A 74 255 255 HOH HOH . D 3 HOH A 75 256 256 HOH HOH . D 3 HOH A 76 257 49 HOH HOH . D 3 HOH A 77 258 50 HOH HOH . D 3 HOH A 78 259 52 HOH HOH . D 3 HOH A 79 260 54 HOH HOH . D 3 HOH A 80 261 261 HOH HOH . D 3 HOH A 81 262 55 HOH HOH . D 3 HOH A 82 263 56 HOH HOH . D 3 HOH A 83 264 59 HOH HOH . D 3 HOH A 84 265 60 HOH HOH . D 3 HOH A 85 266 61 HOH HOH . D 3 HOH A 86 267 63 HOH HOH . D 3 HOH A 87 268 64 HOH HOH . D 3 HOH A 88 269 65 HOH HOH . D 3 HOH A 89 270 68 HOH HOH . D 3 HOH A 90 271 69 HOH HOH . D 3 HOH A 91 272 72 HOH HOH . D 3 HOH A 92 273 73 HOH HOH . D 3 HOH A 93 274 75 HOH HOH . D 3 HOH A 94 275 76 HOH HOH . D 3 HOH A 95 276 77 HOH HOH . D 3 HOH A 96 277 79 HOH HOH . D 3 HOH A 97 278 80 HOH HOH . D 3 HOH A 98 279 81 HOH HOH . D 3 HOH A 99 280 82 HOH HOH . D 3 HOH A 100 281 83 HOH HOH . D 3 HOH A 101 282 84 HOH HOH . D 3 HOH A 102 283 88 HOH HOH . D 3 HOH A 103 284 89 HOH HOH . D 3 HOH A 104 285 90 HOH HOH . D 3 HOH A 105 286 96 HOH HOH . D 3 HOH A 106 287 97 HOH HOH . D 3 HOH A 107 288 98 HOH HOH . D 3 HOH A 108 289 100 HOH HOH . D 3 HOH A 109 290 101 HOH HOH . D 3 HOH A 110 291 102 HOH HOH . D 3 HOH A 111 292 103 HOH HOH . D 3 HOH A 112 293 104 HOH HOH . D 3 HOH A 113 294 105 HOH HOH . D 3 HOH A 114 295 109 HOH HOH . D 3 HOH A 115 296 111 HOH HOH . D 3 HOH A 116 297 112 HOH HOH . D 3 HOH A 117 298 113 HOH HOH . D 3 HOH A 118 299 114 HOH HOH . D 3 HOH A 119 300 115 HOH HOH . D 3 HOH A 120 301 116 HOH HOH . D 3 HOH A 121 302 118 HOH HOH . D 3 HOH A 122 303 119 HOH HOH . D 3 HOH A 123 304 121 HOH HOH . D 3 HOH A 124 305 122 HOH HOH . D 3 HOH A 125 306 124 HOH HOH . D 3 HOH A 126 307 125 HOH HOH . D 3 HOH A 127 308 128 HOH HOH . D 3 HOH A 128 309 131 HOH HOH . D 3 HOH A 129 310 132 HOH HOH . D 3 HOH A 130 311 133 HOH HOH . D 3 HOH A 131 312 134 HOH HOH . D 3 HOH A 132 313 136 HOH HOH . D 3 HOH A 133 314 141 HOH HOH . D 3 HOH A 134 315 144 HOH HOH . D 3 HOH A 135 316 145 HOH HOH . D 3 HOH A 136 317 148 HOH HOH . D 3 HOH A 137 318 150 HOH HOH . D 3 HOH A 138 319 153 HOH HOH . D 3 HOH A 139 320 158 HOH HOH . D 3 HOH A 140 321 165 HOH HOH . D 3 HOH A 141 322 166 HOH HOH . D 3 HOH A 142 323 168 HOH HOH . D 3 HOH A 143 324 169 HOH HOH . D 3 HOH A 144 325 172 HOH HOH . D 3 HOH A 145 326 175 HOH HOH . D 3 HOH A 146 327 176 HOH HOH . D 3 HOH A 147 328 178 HOH HOH . D 3 HOH A 148 329 179 HOH HOH . D 3 HOH A 149 332 106 HOH HOH . D 3 HOH A 150 333 149 HOH HOH . E 3 HOH B 1 182 182 HOH HOH . E 3 HOH B 2 184 184 HOH HOH . E 3 HOH B 3 186 186 HOH HOH . E 3 HOH B 4 187 4 HOH HOH . E 3 HOH B 5 188 188 HOH HOH . E 3 HOH B 6 189 9 HOH HOH . E 3 HOH B 7 190 16 HOH HOH . E 3 HOH B 8 191 191 HOH HOH . E 3 HOH B 9 192 192 HOH HOH . E 3 HOH B 10 193 19 HOH HOH . E 3 HOH B 11 194 30 HOH HOH . E 3 HOH B 12 195 32 HOH HOH . E 3 HOH B 13 196 36 HOH HOH . E 3 HOH B 14 197 41 HOH HOH . E 3 HOH B 15 198 43 HOH HOH . E 3 HOH B 16 199 45 HOH HOH . E 3 HOH B 17 200 46 HOH HOH . E 3 HOH B 18 201 201 HOH HOH . E 3 HOH B 19 202 51 HOH HOH . E 3 HOH B 20 203 53 HOH HOH . E 3 HOH B 21 204 204 HOH HOH . E 3 HOH B 22 205 57 HOH HOH . E 3 HOH B 23 206 58 HOH HOH . E 3 HOH B 24 207 62 HOH HOH . E 3 HOH B 25 208 66 HOH HOH . E 3 HOH B 26 209 67 HOH HOH . E 3 HOH B 27 210 210 HOH HOH . E 3 HOH B 28 211 70 HOH HOH . E 3 HOH B 29 212 71 HOH HOH . E 3 HOH B 30 213 213 HOH HOH . E 3 HOH B 31 214 214 HOH HOH . E 3 HOH B 32 215 215 HOH HOH . E 3 HOH B 33 216 216 HOH HOH . E 3 HOH B 34 217 74 HOH HOH . E 3 HOH B 35 218 218 HOH HOH . E 3 HOH B 36 219 219 HOH HOH . E 3 HOH B 37 220 78 HOH HOH . E 3 HOH B 38 221 85 HOH HOH . E 3 HOH B 39 222 222 HOH HOH . E 3 HOH B 40 223 223 HOH HOH . E 3 HOH B 41 224 87 HOH HOH . E 3 HOH B 42 225 91 HOH HOH . E 3 HOH B 43 226 226 HOH HOH . E 3 HOH B 44 227 92 HOH HOH . E 3 HOH B 45 228 93 HOH HOH . E 3 HOH B 46 229 94 HOH HOH . E 3 HOH B 47 230 230 HOH HOH . E 3 HOH B 48 231 95 HOH HOH . E 3 HOH B 49 232 232 HOH HOH . E 3 HOH B 50 233 99 HOH HOH . E 3 HOH B 51 235 235 HOH HOH . E 3 HOH B 52 236 107 HOH HOH . E 3 HOH B 53 237 237 HOH HOH . E 3 HOH B 54 238 238 HOH HOH . E 3 HOH B 55 239 239 HOH HOH . E 3 HOH B 56 240 240 HOH HOH . E 3 HOH B 57 241 241 HOH HOH . E 3 HOH B 58 242 242 HOH HOH . E 3 HOH B 59 243 108 HOH HOH . E 3 HOH B 60 244 110 HOH HOH . E 3 HOH B 61 245 245 HOH HOH . E 3 HOH B 62 246 246 HOH HOH . E 3 HOH B 63 247 117 HOH HOH . E 3 HOH B 64 248 248 HOH HOH . E 3 HOH B 65 249 120 HOH HOH . E 3 HOH B 66 250 123 HOH HOH . E 3 HOH B 67 251 251 HOH HOH . E 3 HOH B 68 252 126 HOH HOH . E 3 HOH B 69 253 127 HOH HOH . E 3 HOH B 70 254 130 HOH HOH . E 3 HOH B 71 255 135 HOH HOH . E 3 HOH B 72 256 137 HOH HOH . E 3 HOH B 73 257 257 HOH HOH . E 3 HOH B 74 258 258 HOH HOH . E 3 HOH B 75 259 138 HOH HOH . E 3 HOH B 76 260 139 HOH HOH . E 3 HOH B 77 261 140 HOH HOH . E 3 HOH B 78 262 262 HOH HOH . E 3 HOH B 79 263 142 HOH HOH . E 3 HOH B 80 264 143 HOH HOH . E 3 HOH B 81 265 146 HOH HOH . E 3 HOH B 82 267 151 HOH HOH . E 3 HOH B 83 268 152 HOH HOH . E 3 HOH B 84 269 154 HOH HOH . E 3 HOH B 85 270 155 HOH HOH . E 3 HOH B 86 271 156 HOH HOH . E 3 HOH B 87 272 157 HOH HOH . E 3 HOH B 88 273 159 HOH HOH . E 3 HOH B 89 274 161 HOH HOH . E 3 HOH B 90 275 162 HOH HOH . E 3 HOH B 91 276 163 HOH HOH . E 3 HOH B 92 277 164 HOH HOH . E 3 HOH B 93 278 167 HOH HOH . E 3 HOH B 94 279 171 HOH HOH . E 3 HOH B 95 280 173 HOH HOH . E 3 HOH B 96 281 174 HOH HOH . E 3 HOH B 97 282 177 HOH HOH . E 3 HOH B 98 283 180 HOH HOH . E 3 HOH B 99 284 181 HOH HOH . E 3 HOH B 100 330 183 HOH HOH . E 3 HOH B 101 331 185 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 14.699 44.517 -1.08 1 63.7 ? N SAH 4630 A 1 HETATM 2 C CA SAH . . . C 2 14.515 43.097 -0.68 1 71.05 ? CA SAH 4630 A 1 HETATM 3 C CB SAH . . . C 2 13.451 42.42 -1.539 1 75.47 ? CB SAH 4630 A 1 HETATM 4 C CG SAH . . . C 2 13.059 43.147 -2.82 1 74.1 ? CG SAH 4630 A 1 HETATM 5 S SD SAH . . . C 2 12.306 41.998 -3.997 1 39.3 ? SD SAH 4630 A 1 HETATM 6 C C SAH . . . C 2 15.834 42.324 -0.697 1 67.41 ? C SAH 4630 A 1 HETATM 7 O O SAH . . . C 2 16.911 42.912 -0.783 1 64.96 ? O SAH 4630 A 1 HETATM 8 O OXT SAH . . . C 2 15.854 41.097 -0.606 1 66.21 ? OXT SAH 4630 A 1 HETATM 9 C C5' SAH . . . C 2 10.883 43.076 -4.34 1 29.33 ? C5' SAH 4630 A 1 HETATM 10 C C4' SAH . . . C 2 10.127 42.577 -5.567 1 31.12 ? C4' SAH 4630 A 1 HETATM 11 O O4' SAH . . . C 2 8.846 43.168 -5.631 1 33.47 ? O4' SAH 4630 A 1 HETATM 12 C C3' SAH . . . C 2 10.797 42.868 -6.916 1 35.14 ? C3' SAH 4630 A 1 HETATM 13 O O3' SAH . . . C 2 10.969 41.653 -7.621 1 33.05 ? O3' SAH 4630 A 1 HETATM 14 C C2' SAH . . . C 2 9.772 43.709 -7.673 1 34.18 ? C2' SAH 4630 A 1 HETATM 15 O O2' SAH . . . C 2 9.749 43.431 -9.053 1 31.14 ? O2' SAH 4630 A 1 HETATM 16 C C1' SAH . . . C 2 8.489 43.249 -7.002 1 29.11 ? C1' SAH 4630 A 1 HETATM 17 N N9 SAH . . . C 2 7.358 44.171 -7.161 1 33.97 ? N9 SAH 4630 A 1 HETATM 18 C C8 SAH . . . C 2 7.387 45.537 -7.315 1 28.49 ? C8 SAH 4630 A 1 HETATM 19 N N7 SAH . . . C 2 6.109 45.961 -7.4 1 32.69 ? N7 SAH 4630 A 1 HETATM 20 C C5 SAH . . . C 2 5.273 44.903 -7.301 1 33.2 ? C5 SAH 4630 A 1 HETATM 21 C C6 SAH . . . C 2 3.89 44.775 -7.316 1 33.01 ? C6 SAH 4630 A 1 HETATM 22 N N6 SAH . . . C 2 3.103 45.843 -7.456 1 33.74 ? N6 SAH 4630 A 1 HETATM 23 N N1 SAH . . . C 2 3.331 43.523 -7.168 1 36.21 ? N1 SAH 4630 A 1 HETATM 24 C C2 SAH . . . C 2 4.125 42.403 -7.016 1 32.22 ? C2 SAH 4630 A 1 HETATM 25 N N3 SAH . . . C 2 5.495 42.543 -7.003 1 24.95 ? N3 SAH 4630 A 1 HETATM 26 C C4 SAH . . . C 2 6.055 43.768 -7.14 1 31.41 ? C4 SAH 4630 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #