data_6LYH # _model_server_result.job_id gd8Dbit6ha2Icm9kNVtarQ _model_server_result.datetime_utc '2025-03-17 04:38:26' _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":"S","auth_seq_id":501}' # _entry.id 6LYH # _exptl.entry_id 6LYH _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 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 S SD SAH . . . S 2 56.217 16.036 -63.261 1 144.79 ? SD SAH 501 F 1 HETATM 2 C C5' SAH . . . S 2 55.548 14.538 -64.022 1 54.94 ? C5' SAH 501 F 1 HETATM 3 C C4' SAH . . . S 2 54.026 14.554 -64.117 1 65.49 ? C4' SAH 501 F 1 HETATM 4 O O4' SAH . . . S 2 53.57 13.597 -65.059 1 72.88 ? O4' SAH 501 F 1 HETATM 5 C C3' SAH . . . S 2 53.363 14.194 -62.793 1 64.3 ? C3' SAH 501 F 1 HETATM 6 O O3' SAH . . . S 2 52.79 15.333 -62.205 1 63.52 ? O3' SAH 501 F 1 HETATM 7 C C2' SAH . . . S 2 52.277 13.2 -63.144 1 60.87 ? C2' SAH 501 F 1 HETATM 8 O O2' SAH . . . S 2 51.022 13.639 -62.69 1 60.13 ? O2' SAH 501 F 1 HETATM 9 C C1' SAH . . . S 2 52.285 13.161 -64.661 1 69.76 ? C1' SAH 501 F 1 HETATM 10 N N9 SAH . . . S 2 51.969 11.805 -65.138 1 78.41 ? N9 SAH 501 F 1 HETATM 11 C C8 SAH . . . S 2 52.516 10.621 -64.726 1 88.38 ? C8 SAH 501 F 1 HETATM 12 N N7 SAH . . . S 2 51.93 9.621 -65.417 1 92.11 ? N7 SAH 501 F 1 HETATM 13 C C5 SAH . . . S 2 51.012 10.146 -66.257 1 88.07 ? C5 SAH 501 F 1 HETATM 14 C C6 SAH . . . S 2 50.137 9.582 -67.178 1 86.99 ? C6 SAH 501 F 1 HETATM 15 N N6 SAH . . . S 2 50.109 8.266 -67.355 1 98.02 ? N6 SAH 501 F 1 HETATM 16 N N1 SAH . . . S 2 49.299 10.397 -67.911 1 74.92 ? N1 SAH 501 F 1 HETATM 17 C C2 SAH . . . S 2 49.329 11.764 -67.727 1 72.62 ? C2 SAH 501 F 1 HETATM 18 N N3 SAH . . . S 2 50.199 12.32 -66.81 1 71.29 ? N3 SAH 501 F 1 HETATM 19 C C4 SAH . . . S 2 51.027 11.521 -66.089 1 80.05 ? C4 SAH 501 F 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 19 #