data_3NDC
#
_model_server_result.job_id            7a76DdNaLI8GY9_Q00uH_A 
_model_server_result.datetime_utc      '2024-12-27 00:07:20' 
_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          3ndc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","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 . . . D 2 18.897 -38.215 -2.293 1 27.89 ? N SAH 300 B 1 
HETATM 2 C CA SAH . . . D 2 18.757 -38.377 -0.823 1 28.26 ? CA SAH 300 B 1 
HETATM 3 C CB SAH . . . D 2 18.429 -39.85 -0.505 1 28.21 ? CB SAH 300 B 1 
HETATM 4 C CG SAH . . . D 2 17.043 -40.287 -1.03 1 28.83 ? CG SAH 300 B 1 
HETATM 5 S SD SAH . . . D 2 16.698 -41.955 -0.552 1 31.78 ? SD SAH 300 B 1 
HETATM 6 C C SAH . . . D 2 20.027 -37.899 -0.129 1 29.01 ? C SAH 300 B 1 
HETATM 7 O O SAH . . . D 2 20.855 -37.156 -0.677 1 28.41 ? O SAH 300 B 1 
HETATM 8 O OXT SAH . . . D 2 20.291 -38.231 1.023 1 29.69 ? OXT SAH 300 B 1 
HETATM 9 C C5' SAH . . . D 2 15.72 -41.709 0.912 1 29.03 ? C5' SAH 300 B 1 
HETATM 10 C C4' SAH . . . D 2 16.495 -42.165 2.153 1 29.72 ? C4' SAH 300 B 1 
HETATM 11 O O4' SAH . . . D 2 17.459 -41.174 2.556 1 30.65 ? O4' SAH 300 B 1 
HETATM 12 C C3' SAH . . . D 2 15.611 -42.409 3.371 1 29.2 ? C3' SAH 300 B 1 
HETATM 13 O O3' SAH . . . D 2 15.315 -43.793 3.511 1 31.59 ? O3' SAH 300 B 1 
HETATM 14 C C2' SAH . . . D 2 16.474 -42.024 4.543 1 30.24 ? C2' SAH 300 B 1 
HETATM 15 O O2' SAH . . . D 2 17.385 -43.073 4.862 1 31.71 ? O2' SAH 300 B 1 
HETATM 16 C C1' SAH . . . D 2 17.327 -40.937 3.963 1 30.98 ? C1' SAH 300 B 1 
HETATM 17 N N9 SAH . . . D 2 16.832 -39.565 4.266 1 27.29 ? N9 SAH 300 B 1 
HETATM 18 C C8 SAH . . . D 2 16.381 -38.646 3.399 1 26.37 ? C8 SAH 300 B 1 
HETATM 19 N N7 SAH . . . D 2 16.099 -37.477 4.06 1 25.98 ? N7 SAH 300 B 1 
HETATM 20 C C5 SAH . . . D 2 16.389 -37.675 5.362 1 26.47 ? C5 SAH 300 B 1 
HETATM 21 C C6 SAH . . . D 2 16.341 -36.885 6.603 1 26.21 ? C6 SAH 300 B 1 
HETATM 22 N N6 SAH . . . D 2 15.899 -35.604 6.577 1 27.94 ? N6 SAH 300 B 1 
HETATM 23 N N1 SAH . . . D 2 16.725 -37.478 7.741 1 27.5 ? N1 SAH 300 B 1 
HETATM 24 C C2 SAH . . . D 2 17.163 -38.754 7.805 1 28.72 ? C2 SAH 300 B 1 
HETATM 25 N N3 SAH . . . D 2 17.239 -39.532 6.719 1 27.32 ? N3 SAH 300 B 1 
HETATM 26 C C4 SAH . . . D 2 16.869 -39.055 5.495 1 27.37 ? C4 SAH 300 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           319 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           26 
#