data_6PED # _model_server_result.job_id WqRUoaBvnIiYxnvsSkUAdg _model_server_result.datetime_utc '2024-11-20 12:29:49' _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 6ped # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 6PED # _exptl.entry_id 6PED _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 6PED _cell.length_a 110.539 _cell.length_b 110.539 _cell.length_c 131.972 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PED _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _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,E,F,G,H,I,J,K,L,M,N,O _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 6PED _atom_sites.fract_transf_matrix[1][1] 0.009047 _atom_sites.fract_transf_matrix[1][2] 0.005223 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010446 _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] 0.007577 _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 3 SAH A 1 301 301 SAH SAH . D 4 UNX A 1 302 3 UNX UNX . E 4 UNX A 1 303 5 UNX UNX . F 4 UNX A 1 304 6 UNX UNX . G 4 UNX A 1 305 8 UNX UNX . H 4 UNX A 1 306 12 UNX UNX . I 4 UNX A 1 307 13 UNX UNX . J 4 UNX A 1 308 14 UNX UNX . K 4 UNX B 1 201 1 UNX UNX . L 4 UNX B 1 202 4 UNX UNX . M 4 UNX B 1 203 9 UNX UNX . N 4 UNX B 1 204 10 UNX UNX . O 4 UNX B 1 205 11 UNX UNX . # 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 3 15.698 36.227 76.184 1 58.86 ? N SAH 301 A 1 HETATM 2 C CA SAH . . . C 3 15.698 34.887 76.817 1 61.35 ? CA SAH 301 A 1 HETATM 3 C CB SAH . . . C 3 14.7 33.935 76.144 1 51.97 ? CB SAH 301 A 1 HETATM 4 C CG SAH . . . C 3 14.934 33.701 74.715 1 49.61 ? CG SAH 301 A 1 HETATM 5 S SD SAH . . . C 3 13.892 32.314 74.115 1 52.09 ? SD SAH 301 A 1 HETATM 6 C C SAH . . . C 3 17.12 34.297 76.782 1 65.35 ? C SAH 301 A 1 HETATM 7 O O SAH . . . C 3 17.925 34.889 76.053 1 58.34 ? O SAH 301 A 1 HETATM 8 O OXT SAH . . . C 3 17.366 33.285 77.528 1 64.5 ? OXT SAH 301 A 1 HETATM 9 C C5' SAH . . . C 3 12.563 33.201 73.298 1 51.75 ? C5' SAH 301 A 1 HETATM 10 C C4' SAH . . . C 3 11.501 33.804 74.204 1 50.11 ? C4' SAH 301 A 1 HETATM 11 O O4' SAH . . . C 3 10.51 34.396 73.343 1 50 ? O4' SAH 301 A 1 HETATM 12 C C3' SAH . . . C 3 10.762 32.789 75.084 1 47.68 ? C3' SAH 301 A 1 HETATM 13 O O3' SAH . . . C 3 10.765 33.231 76.432 1 53.96 ? O3' SAH 301 A 1 HETATM 14 C C2' SAH . . . C 3 9.378 32.689 74.44 1 44.65 ? C2' SAH 301 A 1 HETATM 15 O O2' SAH . . . C 3 8.395 32.447 75.41 1 46.61 ? O2' SAH 301 A 1 HETATM 16 C C1' SAH . . . C 3 9.23 34.055 73.806 1 50.47 ? C1' SAH 301 A 1 HETATM 17 N N9 SAH . . . C 3 8.334 34.176 72.681 1 51.31 ? N9 SAH 301 A 1 HETATM 18 C C8 SAH . . . C 3 8.081 33.324 71.674 1 50.97 ? C8 SAH 301 A 1 HETATM 19 N N7 SAH . . . C 3 7.18 33.772 70.819 1 49.83 ? N7 SAH 301 A 1 HETATM 20 C C5 SAH . . . C 3 6.831 35.009 71.298 1 43.31 ? C5 SAH 301 A 1 HETATM 21 C C6 SAH . . . C 3 5.927 35.993 70.871 1 51.85 ? C6 SAH 301 A 1 HETATM 22 N N6 SAH . . . C 3 5.148 35.884 69.811 1 51.37 ? N6 SAH 301 A 1 HETATM 23 N N1 SAH . . . C 3 5.81 37.109 71.629 1 50.03 ? N1 SAH 301 A 1 HETATM 24 C C2 SAH . . . C 3 6.56 37.202 72.737 1 50.58 ? C2 SAH 301 A 1 HETATM 25 N N3 SAH . . . C 3 7.465 36.356 73.223 1 48.73 ? N3 SAH 301 A 1 HETATM 26 C C4 SAH . . . C 3 7.55 35.267 72.447 1 52.67 ? C4 SAH 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 26 #