data_5DPL # _model_server_result.job_id 5_SdttVKjsi1j1KQ4FV-6Q _model_server_result.datetime_utc '2024-12-26 12:04:05' _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 5dpl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 5DPL # _exptl.entry_id 5DPL _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 112.3 _cell.angle_gamma 90 _cell.entry_id 5DPL _cell.length_a 83.352 _cell.length_b 91.028 _cell.length_c 105.827 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DPL _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D 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 5DPL _atom_sites.fract_transf_matrix[1][1] 0.011997 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004921 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010986 _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] 0.010214 _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 C 2 SAH A 1 601 1 SAH SAH . D 2 SAH B 1 601 1 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 . . . C 2 87.945 1.34 24.633 1 75.89 ? N SAH 601 A 1 HETATM 2 C CA SAH . . . C 2 88.439 -0.032 24.631 1 83.74 ? CA SAH 601 A 1 HETATM 3 C CB SAH . . . C 2 88.011 -0.749 23.355 1 76.66 ? CB SAH 601 A 1 HETATM 4 C CG SAH . . . C 2 87.591 0.178 22.22 1 77.39 ? CG SAH 601 A 1 HETATM 5 S SD SAH . . . C 2 87.021 -0.732 20.762 1 113.55 ? SD SAH 601 A 1 HETATM 6 C C SAH . . . C 2 89.96 -0.081 24.773 1 88.51 ? C SAH 601 A 1 HETATM 7 O O SAH . . . C 2 90.672 0.788 24.266 1 81.49 ? O SAH 601 A 1 HETATM 8 O OXT SAH . . . C 2 90.512 -0.99 25.397 1 83.37 ? OXT SAH 601 A 1 HETATM 9 C C5' SAH . . . C 2 85.635 0.412 20.542 1 70.88 ? C5' SAH 601 A 1 HETATM 10 C C4' SAH . . . C 2 84.413 -0.028 21.332 1 71.57 ? C4' SAH 601 A 1 HETATM 11 O O4' SAH . . . C 2 83.33 0.869 21.163 1 83.53 ? O4' SAH 601 A 1 HETATM 12 C C3' SAH . . . C 2 83.933 -1.391 20.861 1 78.35 ? C3' SAH 601 A 1 HETATM 13 O O3' SAH . . . C 2 84.236 -2.369 21.828 1 87.29 ? O3' SAH 601 A 1 HETATM 14 C C2' SAH . . . C 2 82.432 -1.251 20.706 1 81.86 ? C2' SAH 601 A 1 HETATM 15 O O2' SAH . . . C 2 81.756 -2.245 21.439 1 71.11 ? O2' SAH 601 A 1 HETATM 16 C C1' SAH . . . C 2 82.121 0.136 21.248 1 81.88 ? C1' SAH 601 A 1 HETATM 17 N N9 SAH . . . C 2 81.009 0.741 20.489 1 76.78 ? N9 SAH 601 A 1 HETATM 18 C C8 SAH . . . C 2 80.913 0.876 19.128 1 73.85 ? C8 SAH 601 A 1 HETATM 19 N N7 SAH . . . C 2 79.732 1.47 18.84 1 80.63 ? N7 SAH 601 A 1 HETATM 20 C C5 SAH . . . C 2 79.07 1.709 19.994 1 69.03 ? C5 SAH 601 A 1 HETATM 21 C C6 SAH . . . C 2 77.835 2.285 20.263 1 69.59 ? C6 SAH 601 A 1 HETATM 22 N N6 SAH . . . C 2 77.077 2.725 19.263 1 82.26 ? N6 SAH 601 A 1 HETATM 23 N N1 SAH . . . C 2 77.404 2.403 21.567 1 66.59 ? N1 SAH 601 A 1 HETATM 24 C C2 SAH . . . C 2 78.206 1.946 22.593 1 73.17 ? C2 SAH 601 A 1 HETATM 25 N N3 SAH . . . C 2 79.432 1.372 22.319 1 72.83 ? N3 SAH 601 A 1 HETATM 26 C C4 SAH . . . C 2 79.859 1.253 21.039 1 70.28 ? C4 SAH 601 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #