data_3TR6
#
_model_server_result.job_id            x-oggHqWs2N2JUVNmiv8PA 
_model_server_result.datetime_utc      '2024-11-08 06:52:50' 
_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          3tr6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":224}' 
#
_entry.id    3TR6 
#
_exptl.entry_id    3TR6 
_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            3TR6 
_cell.length_a            83.686 
_cell.length_b            83.686 
_cell.length_c            212.91 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3TR6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 10_664 -y+1,-x+1,-z-1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 41.843 72.474202 -35.485 
#
_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 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_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
_struct_conn.pdbx_value_order
covale ? covale1 A C MSE 4 A MSE 1 1_555 A N SER 5 A SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale2 A C ALA 45 A ALA 42 1_555 A N MSE 46 A MSE 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale3 A C MSE 46 A MSE 43 1_555 A N GLN 47 A GLN 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale4 A C LEU 62 A LEU 59 1_555 A N MSE 63 A MSE 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale5 A C MSE 63 A MSE 60 1_555 A N GLN 64 A GLN 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale6 A C ALA 81 A ALA 78 1_555 A N MSE 82 A MSE 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale7 A C MSE 82 A MSE 79 1_555 A N GLY 83 A GLY 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale8 A C ASP 208 A ASP 205 1_555 A N MSE 209 A MSE 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale9 A C MSE 209 A MSE 206 1_555 A N ILE 210 A ILE 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
metalc ? metalc1 A OD2 ASP 147 A ASP 144 1_555 B NI NI . A NI 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? 
metalc ? metalc2 A OD2 ASP 173 A ASP 170 1_555 B NI NI . A NI 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? 
metalc ? metalc3 A ND2 ASN 174 A ASN 171 1_555 B NI NI . A NI 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? 
#
_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 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                     3TR6 
_atom_sites.fract_transf_matrix[1][1]    0.011949 
_atom_sites.fract_transf_matrix[1][2]    0.006899 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013798 
_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]    0.004697 
_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
B 2 NI A 1 223 1 NI NI . 
C 3 SAH A 1 224 1 SAH SAH . 
D 4 HOH A 1 225 1 HOH HOH . 
D 4 HOH A 2 226 2 HOH HOH . 
D 4 HOH A 3 227 3 HOH HOH . 
D 4 HOH A 4 228 4 HOH HOH . 
D 4 HOH A 5 229 5 HOH HOH . 
D 4 HOH A 6 230 6 HOH HOH . 
D 4 HOH A 7 231 7 HOH HOH . 
D 4 HOH A 8 232 8 HOH HOH . 
D 4 HOH A 9 233 9 HOH HOH . 
D 4 HOH A 10 234 10 HOH HOH . 
D 4 HOH A 11 235 11 HOH HOH . 
D 4 HOH A 12 236 12 HOH HOH . 
D 4 HOH A 13 237 13 HOH HOH . 
D 4 HOH A 14 238 14 HOH HOH . 
D 4 HOH A 15 239 15 HOH HOH . 
D 4 HOH A 16 240 16 HOH HOH . 
D 4 HOH A 17 241 17 HOH HOH . 
D 4 HOH A 18 242 18 HOH HOH . 
D 4 HOH A 19 243 19 HOH HOH . 
D 4 HOH A 20 244 20 HOH HOH . 
D 4 HOH A 21 245 21 HOH HOH . 
D 4 HOH A 22 246 22 HOH HOH . 
D 4 HOH A 23 247 23 HOH HOH . 
D 4 HOH A 24 248 24 HOH HOH . 
D 4 HOH A 25 249 25 HOH HOH . 
D 4 HOH A 26 250 26 HOH HOH . 
D 4 HOH A 27 251 27 HOH HOH . 
D 4 HOH A 28 252 28 HOH HOH . 
D 4 HOH A 29 253 29 HOH HOH . 
D 4 HOH A 30 254 30 HOH HOH . 
D 4 HOH A 31 255 31 HOH HOH . 
D 4 HOH A 32 256 32 HOH HOH . 
D 4 HOH A 33 257 33 HOH HOH . 
D 4 HOH A 34 258 34 HOH HOH . 
D 4 HOH A 35 259 35 HOH HOH . 
D 4 HOH A 36 260 36 HOH HOH . 
D 4 HOH A 37 261 37 HOH HOH . 
D 4 HOH A 38 262 38 HOH HOH . 
D 4 HOH A 39 263 39 HOH HOH . 
D 4 HOH A 40 264 40 HOH HOH . 
D 4 HOH A 41 265 41 HOH HOH . 
D 4 HOH A 42 266 42 HOH HOH . 
D 4 HOH A 43 267 43 HOH HOH . 
D 4 HOH A 44 268 44 HOH HOH . 
D 4 HOH A 45 269 45 HOH HOH . 
D 4 HOH A 46 270 46 HOH HOH . 
D 4 HOH A 47 271 47 HOH HOH . 
D 4 HOH A 48 272 48 HOH HOH . 
D 4 HOH A 49 273 49 HOH HOH . 
D 4 HOH A 50 274 50 HOH HOH . 
D 4 HOH A 51 275 51 HOH HOH . 
D 4 HOH A 52 276 52 HOH HOH . 
D 4 HOH A 53 277 53 HOH HOH . 
D 4 HOH A 54 278 54 HOH HOH . 
D 4 HOH A 55 279 55 HOH HOH . 
D 4 HOH A 56 280 56 HOH HOH . 
D 4 HOH A 57 281 57 HOH HOH . 
D 4 HOH A 58 282 58 HOH HOH . 
D 4 HOH A 59 283 59 HOH HOH . 
D 4 HOH A 60 284 60 HOH HOH . 
D 4 HOH A 61 285 61 HOH HOH . 
D 4 HOH A 62 286 62 HOH HOH . 
D 4 HOH A 63 287 63 HOH HOH . 
D 4 HOH A 64 288 64 HOH HOH . 
D 4 HOH A 65 289 65 HOH HOH . 
D 4 HOH A 66 290 66 HOH HOH . 
D 4 HOH A 67 291 67 HOH HOH . 
D 4 HOH A 68 292 68 HOH HOH . 
D 4 HOH A 69 293 69 HOH HOH . 
D 4 HOH A 70 294 70 HOH HOH . 
D 4 HOH A 71 295 71 HOH HOH . 
D 4 HOH A 72 296 72 HOH HOH . 
D 4 HOH A 73 297 73 HOH HOH . 
D 4 HOH A 74 298 74 HOH HOH . 
D 4 HOH A 75 299 75 HOH HOH . 
D 4 HOH A 76 300 76 HOH HOH . 
D 4 HOH A 77 301 77 HOH HOH . 
D 4 HOH A 78 302 78 HOH HOH . 
D 4 HOH A 79 303 79 HOH HOH . 
D 4 HOH A 80 304 80 HOH HOH . 
D 4 HOH A 81 305 81 HOH HOH . 
D 4 HOH A 82 306 82 HOH HOH . 
D 4 HOH A 83 307 83 HOH HOH . 
D 4 HOH A 84 308 84 HOH HOH . 
D 4 HOH A 85 309 85 HOH HOH . 
D 4 HOH A 86 310 86 HOH HOH . 
D 4 HOH A 87 311 87 HOH HOH . 
D 4 HOH A 88 312 88 HOH HOH . 
D 4 HOH A 89 313 89 HOH HOH . 
D 4 HOH A 90 314 90 HOH HOH . 
D 4 HOH A 91 315 91 HOH HOH . 
D 4 HOH A 92 316 92 HOH HOH . 
D 4 HOH A 93 317 93 HOH HOH . 
D 4 HOH A 94 318 94 HOH HOH . 
D 4 HOH A 95 319 95 HOH HOH . 
D 4 HOH A 96 320 96 HOH HOH . 
D 4 HOH A 97 321 97 HOH HOH . 
D 4 HOH A 98 322 98 HOH HOH . 
D 4 HOH A 99 323 99 HOH HOH . 
D 4 HOH A 100 324 100 HOH HOH . 
D 4 HOH A 101 325 101 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 7.543 34.458 -2.379 1 35.42 ? N SAH 224 A 1 
HETATM 2 C CA SAH . . . C 3 6.405 34.017 -1.621 1 37.43 ? CA SAH 224 A 1 
HETATM 3 C CB SAH . . . C 3 5.694 35.183 -0.955 1 29.64 ? CB SAH 224 A 1 
HETATM 4 C CG SAH . . . C 3 5.801 35.27 0.55 1 40.52 ? CG SAH 224 A 1 
HETATM 5 S SD SAH . . . C 3 4.798 36.497 1.375 1 37.09 ? SD SAH 224 A 1 
HETATM 6 C C SAH . . . C 3 5.451 33.302 -2.514 1 39.23 ? C SAH 224 A 1 
HETATM 7 O O SAH . . . C 3 4.254 33.152 -2.143 1 39.81 ? O SAH 224 A 1 
HETATM 8 O OXT SAH . . . C 3 5.824 32.85 -3.626 1 34.01 ? OXT SAH 224 A 1 
HETATM 9 C C5' SAH . . . C 3 5.635 37.077 2.842 1 37.87 ? C5' SAH 224 A 1 
HETATM 10 C C4' SAH . . . C 3 6.242 36.086 3.68 1 44.23 ? C4' SAH 224 A 1 
HETATM 11 O O4' SAH . . . C 3 7.306 36.707 4.482 1 41.33 ? O4' SAH 224 A 1 
HETATM 12 C C3' SAH . . . C 3 5.259 35.549 4.644 1 45.83 ? C3' SAH 224 A 1 
HETATM 13 O O3' SAH . . . C 3 5.177 34.192 4.493 1 43.38 ? O3' SAH 224 A 1 
HETATM 14 C C2' SAH . . . C 3 5.794 35.884 5.973 1 49.06 ? C2' SAH 224 A 1 
HETATM 15 O O2' SAH . . . C 3 5.593 34.849 6.852 1 43.11 ? O2' SAH 224 A 1 
HETATM 16 C C1' SAH . . . C 3 7.245 36.072 5.721 1 46.32 ? C1' SAH 224 A 1 
HETATM 17 N N9 SAH . . . C 3 7.977 36.846 6.719 1 48.01 ? N9 SAH 224 A 1 
HETATM 18 C C8 SAH . . . C 3 7.531 37.911 7.403 1 46.66 ? C8 SAH 224 A 1 
HETATM 19 N N7 SAH . . . C 3 8.521 38.326 8.21 1 42.07 ? N7 SAH 224 A 1 
HETATM 20 C C5 SAH . . . C 3 9.594 37.528 8.039 1 46.53 ? C5 SAH 224 A 1 
HETATM 21 C C6 SAH . . . C 3 10.874 37.485 8.6 1 39.75 ? C6 SAH 224 A 1 
HETATM 22 N N6 SAH . . . C 3 11.273 38.436 9.588 1 34.75 ? N6 SAH 224 A 1 
HETATM 23 N N1 SAH . . . C 3 11.727 36.529 8.193 1 44.2 ? N1 SAH 224 A 1 
HETATM 24 C C2 SAH . . . C 3 11.368 35.628 7.269 1 48.99 ? C2 SAH 224 A 1 
HETATM 25 N N3 SAH . . . C 3 10.149 35.641 6.715 1 42.87 ? N3 SAH 224 A 1 
HETATM 26 C C4 SAH . . . C 3 9.248 36.576 7.08 1 49.27 ? C4 SAH 224 A 1 
#
_model_server_stats.io_time_ms              42 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           272 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           26 
#