data_5DST
#
_model_server_result.job_id            N1NRNhF1MB4n_ZP3bJ5tdg 
_model_server_result.datetime_utc      '2024-12-26 11:41:16' 
_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          5dst 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":401}' 
#
_entry.id    5DST 
#
_exptl.entry_id    5DST 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              384.411 
_entity.id                          2 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            S-ADENOSYL-L-HOMOCYSTEINE 
_entity.pdbx_number_of_molecules    15 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          106.48 
_cell.angle_gamma         90 
_cell.entry_id            5DST 
_cell.length_a            199.983 
_cell.length_b            130.943 
_cell.length_c            294.377 
_cell.Z_PDB               60 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5DST 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
PISA dimeric 2 author_and_software_defined_assembly 5 
PISA dimeric 2 author_and_software_defined_assembly 6 
PISA dimeric 2 author_and_software_defined_assembly 7 
PISA dimeric 2 author_and_software_defined_assembly 8 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,P,Q 1 1 
C,D,R,S 2 1 
E,F,T,U 3 1 
G,H,V,W 4 1 
I,J,X,Y 5 1 
K,L,Z,AA 6 1 
M,N,BA,CA 7 1 
O,DA 8 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' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 116.473945 0 282.283644 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 P N N 
? 2 Q N N 
? 2 R N N 
? 2 S N N 
? 2 T N N 
? 2 U N N 
? 2 V N N 
? 2 W N N 
? 2 X N N 
? 2 Y N N 
? 2 Z N N 
? 2 AA N N 
? 2 BA N N 
? 2 CA N N 
? 2 DA 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 275 n n 
N HN1 SAH sing 276 n n 
N HN2 SAH sing 277 n n 
CA CB SAH sing 278 n n 
CA C SAH sing 279 n n 
CA HA SAH sing 280 n n 
CB CG SAH sing 281 n n 
CB HB1 SAH sing 282 n n 
CB HB2 SAH sing 283 n n 
CG SD SAH sing 284 n n 
CG HG1 SAH sing 285 n n 
CG HG2 SAH sing 286 n n 
SD C5' SAH sing 287 n n 
C O SAH doub 288 n n 
C OXT SAH sing 289 n n 
OXT HXT SAH sing 290 n n 
C5' C4' SAH sing 291 n n 
C5' "H5'1" SAH sing 292 n n 
C5' "H5'2" SAH sing 293 n n 
C4' O4' SAH sing 294 n n 
C4' C3' SAH sing 295 n n 
C4' H4' SAH sing 296 n n 
O4' C1' SAH sing 297 n n 
C3' O3' SAH sing 298 n n 
C3' C2' SAH sing 299 n n 
C3' H3' SAH sing 300 n n 
O3' HO3' SAH sing 301 n n 
C2' O2' SAH sing 302 n n 
C2' C1' SAH sing 303 n n 
C2' H2' SAH sing 304 n n 
O2' HO2' SAH sing 305 n n 
C1' N9 SAH sing 306 n n 
C1' H1' SAH sing 307 n n 
N9 C8 SAH sing 308 n y 
N9 C4 SAH sing 309 n y 
C8 N7 SAH doub 310 n y 
C8 H8 SAH sing 311 n n 
N7 C5 SAH sing 312 n y 
C5 C6 SAH sing 313 n y 
C5 C4 SAH doub 314 n y 
C6 N6 SAH sing 315 n n 
C6 N1 SAH doub 316 n y 
N6 HN61 SAH sing 317 n n 
N6 HN62 SAH sing 318 n n 
N1 C2 SAH sing 319 n y 
C2 N3 SAH doub 320 n y 
C2 H2 SAH sing 321 n n 
N3 C4 SAH sing 322 n y 
#
_atom_sites.entry_id                     5DST 
_atom_sites.fract_transf_matrix[1][1]    0.005 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00148 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007637 
_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]    0.003543 
_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
P 2 SAH A 1 401 395 SAH SAH . 
Q 2 SAH B 1 401 395 SAH SAH . 
R 2 SAH C 1 401 395 SAH SAH . 
S 2 SAH D 1 401 395 SAH SAH . 
T 2 SAH E 1 401 395 SAH SAH . 
U 2 SAH F 1 401 395 SAH SAH . 
V 2 SAH G 1 401 395 SAH SAH . 
W 2 SAH H 1 401 395 SAH SAH . 
X 2 SAH I 1 401 395 SAH SAH . 
Y 2 SAH J 1 401 395 SAH SAH . 
Z 2 SAH K 1 401 395 SAH SAH . 
AA 2 SAH L 1 401 395 SAH SAH . 
BA 2 SAH M 1 401 395 SAH SAH . 
CA 2 SAH N 1 401 395 SAH SAH . 
DA 2 SAH O 1 401 395 SAH SAH . 
#
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 . . . R 2 -24.702 -38.006 25.878 1 30.53 ? N SAH 401 C 1 
HETATM 2 C CA SAH . . . R 2 -23.961 -37.775 27.168 1 30.04 ? CA SAH 401 C 1 
HETATM 3 C CB SAH . . . R 2 -23.274 -39.027 27.725 1 28.55 ? CB SAH 401 C 1 
HETATM 4 C CG SAH . . . R 2 -22.221 -39.678 26.838 1 27.47 ? CG SAH 401 C 1 
HETATM 5 S SD SAH . . . R 2 -21.314 -40.866 27.786 1 26.55 ? SD SAH 401 C 1 
HETATM 6 C C SAH . . . R 2 -22.933 -36.696 27.062 1 31.4 ? C SAH 401 C 1 
HETATM 7 O O SAH . . . R 2 -22.486 -36.375 25.952 1 32.23 ? O SAH 401 C 1 
HETATM 8 O OXT SAH . . . R 2 -22.546 -36.113 28.098 1 32.82 ? OXT SAH 401 C 1 
HETATM 9 C C5' SAH . . . R 2 -21.901 -42.435 27.232 1 24.28 ? C5' SAH 401 C 1 
HETATM 10 C C4' SAH . . . R 2 -23.136 -42.818 28.058 1 23.15 ? C4' SAH 401 C 1 
HETATM 11 O O4' SAH . . . R 2 -23.862 -43.923 27.496 1 22.29 ? O4' SAH 401 C 1 
HETATM 12 C C3' SAH . . . R 2 -22.792 -43.241 29.482 1 21.64 ? C3' SAH 401 C 1 
HETATM 13 O O3' SAH . . . R 2 -23.493 -42.379 30.391 1 20.72 ? O3' SAH 401 C 1 
HETATM 14 C C2' SAH . . . R 2 -23.247 -44.681 29.577 1 20.57 ? C2' SAH 401 C 1 
HETATM 15 O O2' SAH . . . R 2 -23.833 -44.966 30.819 1 20.56 ? O2' SAH 401 C 1 
HETATM 16 C C1' SAH . . . R 2 -24.326 -44.77 28.54 1 20.57 ? C1' SAH 401 C 1 
HETATM 17 N N9 SAH . . . R 2 -24.529 -46.114 28.011 1 20.14 ? N9 SAH 401 C 1 
HETATM 18 C C8 SAH . . . R 2 -23.588 -46.888 27.423 1 20.64 ? C8 SAH 401 C 1 
HETATM 19 N N7 SAH . . . R 2 -24.112 -48.071 27.009 1 20.25 ? N7 SAH 401 C 1 
HETATM 20 C C5 SAH . . . R 2 -25.407 -48.015 27.344 1 20.12 ? C5 SAH 401 C 1 
HETATM 21 C C6 SAH . . . R 2 -26.546 -48.902 27.2 1 20.24 ? C6 SAH 401 C 1 
HETATM 22 N N6 SAH . . . R 2 -26.326 -50.098 26.619 1 20.75 ? N6 SAH 401 C 1 
HETATM 23 N N1 SAH . . . R 2 -27.759 -48.486 27.651 1 20.09 ? N1 SAH 401 C 1 
HETATM 24 C C2 SAH . . . R 2 -27.958 -47.299 28.225 1 19.13 ? C2 SAH 401 C 1 
HETATM 25 N N3 SAH . . . R 2 -26.941 -46.453 28.389 1 19.89 ? N3 SAH 401 C 1 
HETATM 26 C C4 SAH . . . R 2 -25.686 -46.739 27.988 1 19.83 ? C4 SAH 401 C 1 
#
_model_server_stats.io_time_ms              42 
_model_server_stats.parse_time_ms           72 
_model_server_stats.create_model_time_ms    75 
_model_server_stats.query_time_ms           1019 
_model_server_stats.encode_time_ms          24 
_model_server_stats.element_count           26 
#