data_6LYH
#
_model_server_result.job_id            1PBVA2z9cj8LdUDsa3qlTA 
_model_server_result.datetime_utc      '2025-07-07 14:04:20' 
_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          6lyh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"U","auth_seq_id":501}' 
#
_entry.id    6LYH 
#
_exptl.entry_id    6LYH 
_exptl.method      'X-RAY DIFFRACTION' 
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_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    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90.211 
_cell.angle_beta          90.039 
_cell.angle_gamma         90.172 
_cell.entry_id            6LYH 
_cell.length_a            87.744 
_cell.length_b            86.812 
_cell.length_c            123.258 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6LYH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    'P 1' 
_symmetry.space_group_name_H-M     'P 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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,I,J 1 1 
C,M,N 1 2 
B,D,K,L,O,P 2 1 
E,Q,R 3 1 
G,U,V 3 3 
F,S,T 4 1 
H,W,X 4 4 
#
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' 1_455 x-1,y,z 1 0 0 0 1 0 0 0 1 -87.744 0 0 
3 'crystal symmetry operation' 1_655 x+1,y,z 1 0 0 0 1 0 0 0 1 87.744 0 0 
4 'crystal symmetry operation' 1_565 x,y+1,z 1 0 0 0 1 0 0 0 1 -0.260606 86.811609 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 I N N 
? 2 K N N 
? 2 M N N 
? 2 O N N 
? 2 Q N N 
? 2 S N N 
? 2 U N N 
? 2 W 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 301 n n 
N HN1 SAH sing 302 n n 
N HN2 SAH sing 303 n n 
CA CB SAH sing 304 n n 
CA C SAH sing 305 n n 
CA HA SAH sing 306 n n 
CB CG SAH sing 307 n n 
CB HB1 SAH sing 308 n n 
CB HB2 SAH sing 309 n n 
CG SD SAH sing 310 n n 
CG HG1 SAH sing 311 n n 
CG HG2 SAH sing 312 n n 
SD C5' SAH sing 313 n n 
C O SAH doub 314 n n 
C OXT SAH sing 315 n n 
OXT HXT SAH sing 316 n n 
C5' C4' SAH sing 317 n n 
C5' "H5'1" SAH sing 318 n n 
C5' "H5'2" SAH sing 319 n n 
C4' O4' SAH sing 320 n n 
C4' C3' SAH sing 321 n n 
C4' H4' SAH sing 322 n n 
O4' C1' SAH sing 323 n n 
C3' O3' SAH sing 324 n n 
C3' C2' SAH sing 325 n n 
C3' H3' SAH sing 326 n n 
O3' HO3' SAH sing 327 n n 
C2' O2' SAH sing 328 n n 
C2' C1' SAH sing 329 n n 
C2' H2' SAH sing 330 n n 
O2' HO2' SAH sing 331 n n 
C1' N9 SAH sing 332 n n 
C1' H1' SAH sing 333 n n 
N9 C8 SAH sing 334 n y 
N9 C4 SAH sing 335 n y 
C8 N7 SAH doub 336 n y 
C8 H8 SAH sing 337 n n 
N7 C5 SAH sing 338 n y 
C5 C6 SAH sing 339 n y 
C5 C4 SAH doub 340 n y 
C6 N6 SAH sing 341 n n 
C6 N1 SAH doub 342 n y 
N6 HN61 SAH sing 343 n n 
N6 HN62 SAH sing 344 n n 
N1 C2 SAH sing 345 n y 
C2 N3 SAH doub 346 n y 
C2 H2 SAH sing 347 n n 
N3 C4 SAH sing 348 n y 
#
_atom_sites.entry_id                     6LYH 
_atom_sites.fract_transf_matrix[1][1]    0.011397 
_atom_sites.fract_transf_matrix[1][2]    0.000034 
_atom_sites.fract_transf_matrix[1][3]    0.000008 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011519 
_atom_sites.fract_transf_matrix[2][3]    0.000042 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.008113 
_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
I 2 SAH B 1 501 501 SAH SAH . 
J 3 EXU B 1 502 601 EXU DRG . 
K 2 SAH A 1 501 501 SAH SAH . 
L 3 EXU A 1 502 601 EXU DRG . 
M 2 SAH C 1 501 501 SAH SAH . 
N 3 EXU C 1 502 601 EXU DRG . 
O 2 SAH D 1 501 501 SAH SAH . 
P 3 EXU D 1 502 601 EXU DRG . 
Q 2 SAH E 1 501 501 SAH SAH . 
R 3 EXU E 1 502 601 EXU DRG . 
S 2 SAH F 1 501 501 SAH SAH . 
T 3 EXU F 1 502 601 EXU DRG . 
U 2 SAH G 1 501 501 SAH SAH . 
V 3 EXU G 1 502 601 EXU DRG . 
W 2 SAH H 1 501 501 SAH SAH . 
X 3 EXU H 1 502 601 EXU DRG . 
#
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 . . . U 2 0.301 -13.755 -126.206 1 0.78 ? N SAH 501 G 1 
HETATM 2 C CA SAH . . . U 2 -0.609 -14.457 -127.099 1 29.01 ? CA SAH 501 G 1 
HETATM 3 C CB SAH . . . U 2 -1.777 -15.057 -126.322 1 40.04 ? CB SAH 501 G 1 
HETATM 4 C CG SAH . . . U 2 -1.579 -16.526 -125.948 1 20.6 ? CG SAH 501 G 1 
HETATM 5 S SD SAH . . . U 2 -2.56 -17.062 -124.526 1 128.72 ? SD SAH 501 G 1 
HETATM 6 C C SAH . . . U 2 -1.094 -13.546 -128.222 1 49.12 ? C SAH 501 G 1 
HETATM 7 O O SAH . . . U 2 -2.078 -13.833 -128.906 1 59.74 ? O SAH 501 G 1 
HETATM 8 O OXT SAH . . . U 2 -0.508 -12.495 -128.475 1 71.59 ? OXT SAH 501 G 1 
HETATM 9 C C5' SAH . . . U 2 -3.327 -18.392 -125.476 1 10.24 ? C5' SAH 501 G 1 
HETATM 10 C C4' SAH . . . U 2 -4.838 -18.223 -125.609 1 36.42 ? C4' SAH 501 G 1 
HETATM 11 O O4' SAH . . . U 2 -5.354 -19.117 -126.585 1 39.21 ? O4' SAH 501 G 1 
HETATM 12 C C3' SAH . . . U 2 -5.561 -18.553 -124.306 1 36.73 ? C3' SAH 501 G 1 
HETATM 13 O O3' SAH . . . U 2 -6.149 -17.404 -123.743 1 29.79 ? O3' SAH 501 G 1 
HETATM 14 C C2' SAH . . . U 2 -6.635 -19.558 -124.669 1 21.38 ? C2' SAH 501 G 1 
HETATM 15 O O2' SAH . . . U 2 -7.895 -19.134 -124.22 1 21.48 ? O2' SAH 501 G 1 
HETATM 16 C C1' SAH . . . U 2 -6.619 -19.613 -126.184 1 24.01 ? C1' SAH 501 G 1 
HETATM 17 N N9 SAH . . . U 2 -6.841 -20.994 -126.648 1 25.51 ? N9 SAH 501 G 1 
HETATM 18 C C8 SAH . . . U 2 -6.231 -22.136 -126.205 1 44.48 ? C8 SAH 501 G 1 
HETATM 19 N N7 SAH . . . U 2 -6.734 -23.181 -126.892 1 41.3 ? N7 SAH 501 G 1 
HETATM 20 C C5 SAH . . . U 2 -7.658 -22.727 -127.764 1 31.02 ? C5 SAH 501 G 1 
HETATM 21 C C6 SAH . . . U 2 -8.468 -23.362 -128.697 1 39.17 ? C6 SAH 501 G 1 
HETATM 22 N N6 SAH . . . U 2 -8.41 -24.682 -128.857 1 67.41 ? N6 SAH 501 G 1 
HETATM 23 N N1 SAH . . . U 2 -9.334 -22.608 -129.462 1 16.21 ? N1 SAH 501 G 1 
HETATM 24 C C2 SAH . . . U 2 -9.398 -21.239 -129.3 1 25.33 ? C2 SAH 501 G 1 
HETATM 25 N N3 SAH . . . U 2 -8.592 -20.612 -128.373 1 27.45 ? N3 SAH 501 G 1 
HETATM 26 C C4 SAH . . . U 2 -7.736 -21.349 -127.62 1 26.78 ? C4 SAH 501 G 1 
#
_model_server_stats.io_time_ms              56 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           26 
#