data_5DST # _model_server_result.job_id H_hhqWHeyPv7q5_756LBew _model_server_result.datetime_utc '2024-12-26 11:09:22' _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":"T","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 . . . T 2 37.886 -42.934 22.756 1 34.41 ? N SAH 401 E 1 HETATM 2 C CA SAH . . . T 2 38.493 -43.108 24.109 1 35.64 ? CA SAH 401 E 1 HETATM 3 C CB SAH . . . T 2 39.959 -42.679 24.128 1 36.29 ? CB SAH 401 E 1 HETATM 4 C CG SAH . . . T 2 40.166 -41.295 23.501 1 36.67 ? CG SAH 401 E 1 HETATM 5 S SD SAH . . . T 2 41.591 -40.491 24.168 1 35.51 ? SD SAH 401 E 1 HETATM 6 C C SAH . . . T 2 37.762 -42.295 25.141 1 35.75 ? C SAH 401 E 1 HETATM 7 O O SAH . . . T 2 37.013 -41.41 24.684 1 32 ? O SAH 401 E 1 HETATM 8 O OXT SAH . . . T 2 37.931 -42.506 26.387 1 33.9 ? OXT SAH 401 E 1 HETATM 9 C C5' SAH . . . T 2 42.749 -40.651 22.849 1 33.4 ? C5' SAH 401 E 1 HETATM 10 C C4' SAH . . . T 2 43.434 -41.988 23.071 1 32.42 ? C4' SAH 401 E 1 HETATM 11 O O4' SAH . . . T 2 44.248 -42.366 21.97 1 31.08 ? O4' SAH 401 E 1 HETATM 12 C C3' SAH . . . T 2 44.32 -41.959 24.31 1 31.17 ? C3' SAH 401 E 1 HETATM 13 O O3' SAH . . . T 2 43.897 -43.042 25.15 1 29.8 ? O3' SAH 401 E 1 HETATM 14 C C2' SAH . . . T 2 45.737 -42.11 23.791 1 30.44 ? C2' SAH 401 E 1 HETATM 15 O O2' SAH . . . T 2 46.543 -42.914 24.65 1 30.54 ? O2' SAH 401 E 1 HETATM 16 C C1' SAH . . . T 2 45.491 -42.831 22.489 1 30.41 ? C1' SAH 401 E 1 HETATM 17 N N9 SAH . . . T 2 46.454 -42.61 21.414 1 29.55 ? N9 SAH 401 E 1 HETATM 18 C C8 SAH . . . T 2 46.873 -41.443 20.901 1 28.31 ? C8 SAH 401 E 1 HETATM 19 N N7 SAH . . . T 2 47.72 -41.685 19.879 1 28.83 ? N7 SAH 401 E 1 HETATM 20 C C5 SAH . . . T 2 47.832 -43.03 19.741 1 30.61 ? C5 SAH 401 E 1 HETATM 21 C C6 SAH . . . T 2 48.548 -43.992 18.862 1 30.67 ? C6 SAH 401 E 1 HETATM 22 N N6 SAH . . . T 2 49.349 -43.519 17.89 1 30.98 ? N6 SAH 401 E 1 HETATM 23 N N1 SAH . . . T 2 48.374 -45.327 19.041 1 30.96 ? N1 SAH 401 E 1 HETATM 24 C C2 SAH . . . T 2 47.558 -45.815 19.997 1 31.21 ? C2 SAH 401 E 1 HETATM 25 N N3 SAH . . . T 2 46.871 -45.02 20.846 1 31.94 ? N3 SAH 401 E 1 HETATM 26 C C4 SAH . . . T 2 46.972 -43.645 20.756 1 31.3 ? C4 SAH 401 E 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #