data_2PBF
#
_model_server_result.job_id            z6yZRnqjPDPnXF_ZXvs-Rw 
_model_server_result.datetime_utc      '2024-10-16 10:37:35' 
_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          2pbf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":301}' 
#
_entry.id    2PBF 
#
_exptl.entry_id    2PBF 
_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            2PBF 
_cell.length_a            75.156 
_cell.length_b            75.156 
_cell.length_c            77.389 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2PBF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        145 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E 1 1 
B,D,F 2 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                     2PBF 
_atom_sites.fract_transf_matrix[1][1]    0.013306 
_atom_sites.fract_transf_matrix[1][2]    0.007682 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015364 
_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]    0.012922 
_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 2 SAH B 1 301 301 SAH SAH . 
E 3 HOH A 1 302 1 HOH HOH . 
E 3 HOH A 2 303 2 HOH HOH . 
E 3 HOH A 3 304 3 HOH HOH . 
E 3 HOH A 4 305 4 HOH HOH . 
E 3 HOH A 5 306 5 HOH HOH . 
E 3 HOH A 6 307 6 HOH HOH . 
E 3 HOH A 7 308 7 HOH HOH . 
E 3 HOH A 8 309 8 HOH HOH . 
E 3 HOH A 9 310 9 HOH HOH . 
E 3 HOH A 10 311 10 HOH HOH . 
E 3 HOH A 11 312 11 HOH HOH . 
E 3 HOH A 12 313 12 HOH HOH . 
E 3 HOH A 13 314 13 HOH HOH . 
E 3 HOH A 14 315 14 HOH HOH . 
E 3 HOH A 15 316 15 HOH HOH . 
E 3 HOH A 16 317 16 HOH HOH . 
E 3 HOH A 17 318 17 HOH HOH . 
E 3 HOH A 18 319 18 HOH HOH . 
E 3 HOH A 19 320 19 HOH HOH . 
E 3 HOH A 20 321 20 HOH HOH . 
E 3 HOH A 21 322 21 HOH HOH . 
E 3 HOH A 22 323 22 HOH HOH . 
E 3 HOH A 23 324 23 HOH HOH . 
E 3 HOH A 24 325 24 HOH HOH . 
E 3 HOH A 25 326 25 HOH HOH . 
E 3 HOH A 26 327 26 HOH HOH . 
E 3 HOH A 27 328 27 HOH HOH . 
E 3 HOH A 28 329 28 HOH HOH . 
E 3 HOH A 29 330 30 HOH HOH . 
E 3 HOH A 30 331 31 HOH HOH . 
E 3 HOH A 31 332 32 HOH HOH . 
E 3 HOH A 32 333 33 HOH HOH . 
E 3 HOH A 33 334 34 HOH HOH . 
E 3 HOH A 34 335 35 HOH HOH . 
E 3 HOH A 35 336 36 HOH HOH . 
E 3 HOH A 36 337 37 HOH HOH . 
E 3 HOH A 37 338 38 HOH HOH . 
E 3 HOH A 38 339 39 HOH HOH . 
E 3 HOH A 39 340 40 HOH HOH . 
E 3 HOH A 40 341 41 HOH HOH . 
E 3 HOH A 41 342 42 HOH HOH . 
E 3 HOH A 42 343 43 HOH HOH . 
E 3 HOH A 43 344 44 HOH HOH . 
E 3 HOH A 44 345 45 HOH HOH . 
E 3 HOH A 45 346 46 HOH HOH . 
E 3 HOH A 46 347 47 HOH HOH . 
E 3 HOH A 47 348 48 HOH HOH . 
E 3 HOH A 48 349 49 HOH HOH . 
E 3 HOH A 49 350 50 HOH HOH . 
E 3 HOH A 50 351 51 HOH HOH . 
E 3 HOH A 51 352 52 HOH HOH . 
E 3 HOH A 52 353 53 HOH HOH . 
E 3 HOH A 53 354 54 HOH HOH . 
E 3 HOH A 54 355 55 HOH HOH . 
E 3 HOH A 55 356 56 HOH HOH . 
E 3 HOH A 56 357 57 HOH HOH . 
E 3 HOH A 57 358 58 HOH HOH . 
E 3 HOH A 58 359 59 HOH HOH . 
E 3 HOH A 59 360 61 HOH HOH . 
E 3 HOH A 60 361 62 HOH HOH . 
E 3 HOH A 61 362 63 HOH HOH . 
E 3 HOH A 62 363 64 HOH HOH . 
E 3 HOH A 63 364 65 HOH HOH . 
E 3 HOH A 64 365 66 HOH HOH . 
E 3 HOH A 65 366 67 HOH HOH . 
E 3 HOH A 66 367 68 HOH HOH . 
E 3 HOH A 67 368 69 HOH HOH . 
E 3 HOH A 68 369 70 HOH HOH . 
E 3 HOH A 69 370 71 HOH HOH . 
E 3 HOH A 70 371 72 HOH HOH . 
E 3 HOH A 71 372 73 HOH HOH . 
E 3 HOH A 72 373 74 HOH HOH . 
E 3 HOH A 73 374 75 HOH HOH . 
E 3 HOH A 74 375 76 HOH HOH . 
E 3 HOH A 75 376 77 HOH HOH . 
E 3 HOH A 76 377 78 HOH HOH . 
E 3 HOH A 77 378 79 HOH HOH . 
E 3 HOH A 78 379 80 HOH HOH . 
E 3 HOH A 79 380 81 HOH HOH . 
E 3 HOH A 80 381 82 HOH HOH . 
E 3 HOH A 81 382 83 HOH HOH . 
E 3 HOH A 82 383 84 HOH HOH . 
E 3 HOH A 83 384 85 HOH HOH . 
E 3 HOH A 84 385 86 HOH HOH . 
E 3 HOH A 85 386 87 HOH HOH . 
E 3 HOH A 86 387 88 HOH HOH . 
E 3 HOH A 87 388 89 HOH HOH . 
E 3 HOH A 88 389 90 HOH HOH . 
E 3 HOH A 89 390 91 HOH HOH . 
E 3 HOH A 90 391 92 HOH HOH . 
E 3 HOH A 91 392 121 HOH HOH . 
E 3 HOH A 92 393 151 HOH HOH . 
F 3 HOH B 1 302 29 HOH HOH . 
F 3 HOH B 2 303 60 HOH HOH . 
F 3 HOH B 3 304 93 HOH HOH . 
F 3 HOH B 4 305 94 HOH HOH . 
F 3 HOH B 5 306 95 HOH HOH . 
F 3 HOH B 6 307 96 HOH HOH . 
F 3 HOH B 7 308 97 HOH HOH . 
F 3 HOH B 8 309 98 HOH HOH . 
F 3 HOH B 9 310 99 HOH HOH . 
F 3 HOH B 10 311 100 HOH HOH . 
F 3 HOH B 11 312 101 HOH HOH . 
F 3 HOH B 12 313 102 HOH HOH . 
F 3 HOH B 13 314 103 HOH HOH . 
F 3 HOH B 14 315 104 HOH HOH . 
F 3 HOH B 15 316 105 HOH HOH . 
F 3 HOH B 16 317 106 HOH HOH . 
F 3 HOH B 17 318 107 HOH HOH . 
F 3 HOH B 18 319 108 HOH HOH . 
F 3 HOH B 19 320 109 HOH HOH . 
F 3 HOH B 20 321 110 HOH HOH . 
F 3 HOH B 21 322 111 HOH HOH . 
F 3 HOH B 22 323 112 HOH HOH . 
F 3 HOH B 23 324 113 HOH HOH . 
F 3 HOH B 24 325 114 HOH HOH . 
F 3 HOH B 25 326 115 HOH HOH . 
F 3 HOH B 26 327 116 HOH HOH . 
F 3 HOH B 27 328 117 HOH HOH . 
F 3 HOH B 28 329 118 HOH HOH . 
F 3 HOH B 29 330 119 HOH HOH . 
F 3 HOH B 30 331 120 HOH HOH . 
F 3 HOH B 31 332 122 HOH HOH . 
F 3 HOH B 32 333 123 HOH HOH . 
F 3 HOH B 33 334 124 HOH HOH . 
F 3 HOH B 34 335 125 HOH HOH . 
F 3 HOH B 35 336 126 HOH HOH . 
F 3 HOH B 36 337 127 HOH HOH . 
F 3 HOH B 37 338 128 HOH HOH . 
F 3 HOH B 38 339 129 HOH HOH . 
F 3 HOH B 39 340 130 HOH HOH . 
F 3 HOH B 40 341 131 HOH HOH . 
F 3 HOH B 41 342 132 HOH HOH . 
F 3 HOH B 42 343 133 HOH HOH . 
F 3 HOH B 43 344 134 HOH HOH . 
F 3 HOH B 44 345 135 HOH HOH . 
F 3 HOH B 45 346 136 HOH HOH . 
F 3 HOH B 46 347 137 HOH HOH . 
F 3 HOH B 47 348 138 HOH HOH . 
F 3 HOH B 48 349 139 HOH HOH . 
F 3 HOH B 49 350 140 HOH HOH . 
F 3 HOH B 50 351 141 HOH HOH . 
F 3 HOH B 51 352 142 HOH HOH . 
F 3 HOH B 52 353 143 HOH HOH . 
F 3 HOH B 53 354 144 HOH HOH . 
F 3 HOH B 54 355 145 HOH HOH . 
F 3 HOH B 55 356 146 HOH HOH . 
F 3 HOH B 56 357 147 HOH HOH . 
F 3 HOH B 57 358 148 HOH HOH . 
F 3 HOH B 58 359 149 HOH HOH . 
F 3 HOH B 59 360 150 HOH HOH . 
F 3 HOH B 60 361 152 HOH HOH . 
F 3 HOH B 61 362 153 HOH HOH . 
F 3 HOH B 62 363 154 HOH HOH . 
F 3 HOH B 63 364 155 HOH HOH . 
F 3 HOH B 64 365 156 HOH HOH . 
F 3 HOH B 65 366 157 HOH HOH . 
F 3 HOH B 66 367 158 HOH HOH . 
F 3 HOH B 67 368 159 HOH HOH . 
F 3 HOH B 68 369 160 HOH HOH . 
F 3 HOH B 69 370 161 HOH HOH . 
F 3 HOH B 70 371 162 HOH HOH . 
F 3 HOH B 71 372 163 HOH HOH . 
F 3 HOH B 72 373 164 HOH HOH . 
F 3 HOH B 73 374 165 HOH HOH . 
F 3 HOH B 74 375 166 HOH HOH . 
F 3 HOH B 75 376 167 HOH HOH . 
F 3 HOH B 76 377 168 HOH HOH . 
F 3 HOH B 77 378 169 HOH HOH . 
F 3 HOH B 78 379 170 HOH HOH . 
F 3 HOH B 79 380 171 HOH HOH . 
F 3 HOH B 80 381 172 HOH HOH . 
F 3 HOH B 81 382 173 HOH HOH . 
F 3 HOH B 82 383 174 HOH HOH . 
F 3 HOH B 83 384 175 HOH HOH . 
F 3 HOH B 84 385 176 HOH HOH . 
F 3 HOH B 85 386 177 HOH HOH . 
F 3 HOH B 86 387 178 HOH HOH . 
F 3 HOH B 87 388 179 HOH HOH . 
F 3 HOH B 88 389 180 HOH HOH . 
F 3 HOH B 89 390 181 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 27.581 0.315 -29.953 1 27.64 ? N SAH 301 B 1 
HETATM 2 C CA SAH . . . D 2 28.736 0.006 -29.059 1 27.65 ? CA SAH 301 B 1 
HETATM 3 C CB SAH . . . D 2 28.674 0.938 -27.883 1 27.06 ? CB SAH 301 B 1 
HETATM 4 C CG SAH . . . D 2 30.047 1.021 -27.211 1 29.17 ? CG SAH 301 B 1 
HETATM 5 S SD SAH . . . D 2 29.966 2.035 -25.727 1 30.36 ? SD SAH 301 B 1 
HETATM 6 C C SAH . . . D 2 28.761 -1.437 -28.55 1 27.18 ? C SAH 301 B 1 
HETATM 7 O O SAH . . . D 2 27.702 -1.956 -28.185 1 26.24 ? O SAH 301 B 1 
HETATM 8 O OXT SAH . . . D 2 29.818 -2.103 -28.484 1 26.94 ? OXT SAH 301 B 1 
HETATM 9 C C5' SAH . . . D 2 30.156 3.627 -26.569 1 30.2 ? C5' SAH 301 B 1 
HETATM 10 C C4' SAH . . . D 2 31.421 3.723 -27.428 1 29.35 ? C4' SAH 301 B 1 
HETATM 11 O O4' SAH . . . D 2 31.513 5.043 -27.865 1 31.23 ? O4' SAH 301 B 1 
HETATM 12 C C3' SAH . . . D 2 32.72 3.399 -26.7 1 29.65 ? C3' SAH 301 B 1 
HETATM 13 O O3' SAH . . . D 2 33.416 2.33 -27.324 1 28.28 ? O3' SAH 301 B 1 
HETATM 14 C C2' SAH . . . D 2 33.493 4.719 -26.696 1 29.43 ? C2' SAH 301 B 1 
HETATM 15 O O2' SAH . . . D 2 34.885 4.547 -26.812 1 29.17 ? O2' SAH 301 B 1 
HETATM 16 C C1' SAH . . . D 2 32.889 5.425 -27.887 1 30.3 ? C1' SAH 301 B 1 
HETATM 17 N N9 SAH . . . D 2 32.998 6.913 -27.89 1 30.33 ? N9 SAH 301 B 1 
HETATM 18 C C8 SAH . . . D 2 32.801 7.782 -26.848 1 30.85 ? C8 SAH 301 B 1 
HETATM 19 N N7 SAH . . . D 2 32.945 9.055 -27.308 1 31.68 ? N7 SAH 301 B 1 
HETATM 20 C C5 SAH . . . D 2 33.25 9.003 -28.628 1 30.42 ? C5 SAH 301 B 1 
HETATM 21 C C6 SAH . . . D 2 33.526 9.978 -29.585 1 31.19 ? C6 SAH 301 B 1 
HETATM 22 N N6 SAH . . . D 2 33.537 11.265 -29.282 1 28.67 ? N6 SAH 301 B 1 
HETATM 23 N N1 SAH . . . D 2 33.782 9.598 -30.884 1 31.11 ? N1 SAH 301 B 1 
HETATM 24 C C2 SAH . . . D 2 33.781 8.271 -31.245 1 29.56 ? C2 SAH 301 B 1 
HETATM 25 N N3 SAH . . . D 2 33.528 7.324 -30.289 1 30.56 ? N3 SAH 301 B 1 
HETATM 26 C C4 SAH . . . D 2 33.265 7.668 -29.003 1 29.94 ? C4 SAH 301 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           258 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           26 
#