data_6GKY # _model_server_result.job_id V-khB1CkcFB77SIG0YGhDA _model_server_result.datetime_utc '2024-12-28 02:13:29' _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 6gky # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 6GKY # _exptl.entry_id 6GKY _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 90 _cell.angle_gamma 90 _cell.entry_id 6GKY _cell.length_a 48.295 _cell.length_b 95.957 _cell.length_c 154.567 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6GKY _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression B,E,F 1 1 A,C,D 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_455 -x-1/2,-y,z+1/2 -1 0 0 0 -1 0 0 0 1 -24.1475 0 77.2835 # 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 E 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 304 n n N HN1 SAH sing 305 n n N HN2 SAH sing 306 n n CA CB SAH sing 307 n n CA C SAH sing 308 n n CA HA SAH sing 309 n n CB CG SAH sing 310 n n CB HB1 SAH sing 311 n n CB HB2 SAH sing 312 n n CG SD SAH sing 313 n n CG HG1 SAH sing 314 n n CG HG2 SAH sing 315 n n SD C5' SAH sing 316 n n C O SAH doub 317 n n C OXT SAH sing 318 n n OXT HXT SAH sing 319 n n C5' C4' SAH sing 320 n n C5' "H5'1" SAH sing 321 n n C5' "H5'2" SAH sing 322 n n C4' O4' SAH sing 323 n n C4' C3' SAH sing 324 n n C4' H4' SAH sing 325 n n O4' C1' SAH sing 326 n n C3' O3' SAH sing 327 n n C3' C2' SAH sing 328 n n C3' H3' SAH sing 329 n n O3' HO3' SAH sing 330 n n C2' O2' SAH sing 331 n n C2' C1' SAH sing 332 n n C2' H2' SAH sing 333 n n O2' HO2' SAH sing 334 n n C1' N9 SAH sing 335 n n C1' H1' SAH sing 336 n n N9 C8 SAH sing 337 n y N9 C4 SAH sing 338 n y C8 N7 SAH doub 339 n y C8 H8 SAH sing 340 n n N7 C5 SAH sing 341 n y C5 C6 SAH sing 342 n y C5 C4 SAH doub 343 n y C6 N6 SAH sing 344 n n C6 N1 SAH doub 345 n y N6 HN61 SAH sing 346 n n N6 HN62 SAH sing 347 n n N1 C2 SAH sing 348 n y C2 N3 SAH doub 349 n y C2 H2 SAH sing 350 n n N3 C4 SAH sing 351 n y # _atom_sites.entry_id 6GKY _atom_sites.fract_transf_matrix[1][1] 0.020706 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010421 _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] 0.00647 _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 1 501 501 SAH SAH . D 3 F2Z A 1 502 998 F2Z DRG . E 2 SAH B 1 501 501 SAH SAH . F 3 F2Z B 1 502 998 F2Z 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 . . . C 2 26.619 27.83 -20.243 1 64.24 ? N SAH 501 A 1 HETATM 2 C CA SAH . . . C 2 27.263 27.022 -19.214 1 70.96 ? CA SAH 501 A 1 HETATM 3 C CB SAH . . . C 2 26.255 26.625 -18.142 1 79.29 ? CB SAH 501 A 1 HETATM 4 C CG SAH . . . C 2 24.917 26.139 -18.686 1 77.54 ? CG SAH 501 A 1 HETATM 5 S SD SAH . . . C 2 23.775 25.675 -17.362 1 93.4 ? SD SAH 501 A 1 HETATM 6 C C SAH . . . C 2 27.923 25.784 -19.81 1 80.73 ? C SAH 501 A 1 HETATM 7 O O SAH . . . C 2 27.652 25.407 -20.949 1 81.19 ? O SAH 501 A 1 HETATM 8 O OXT SAH . . . C 2 28.745 25.132 -19.165 1 88.32 ? OXT SAH 501 A 1 HETATM 9 C C5' SAH . . . C 2 22.781 27.147 -17.71 1 70.38 ? C5' SAH 501 A 1 HETATM 10 C C4' SAH . . . C 2 23.381 28.411 -17.104 1 87.57 ? C4' SAH 501 A 1 HETATM 11 O O4' SAH . . . C 2 22.494 29.5 -17.28 1 88.08 ? O4' SAH 501 A 1 HETATM 12 C C3' SAH . . . C 2 23.626 28.254 -15.611 1 98.07 ? C3' SAH 501 A 1 HETATM 13 O O3' SAH . . . C 2 25.001 28.38 -15.332 1 99.02 ? O3' SAH 501 A 1 HETATM 14 C C2' SAH . . . C 2 22.865 29.382 -14.948 1 90.69 ? C2' SAH 501 A 1 HETATM 15 O O2' SAH . . . C 2 23.711 30.105 -14.086 1 88.52 ? O2' SAH 501 A 1 HETATM 16 C C1' SAH . . . C 2 22.4 30.265 -16.094 1 85.91 ? C1' SAH 501 A 1 HETATM 17 N N9 SAH . . . C 2 21.014 30.718 -15.871 1 85.15 ? N9 SAH 501 A 1 HETATM 18 C C8 SAH . . . C 2 19.923 29.923 -15.637 1 89.3 ? C8 SAH 501 A 1 HETATM 19 N N7 SAH . . . C 2 18.838 30.716 -15.481 1 89.86 ? N7 SAH 501 A 1 HETATM 20 C C5 SAH . . . C 2 19.222 32.006 -15.608 1 82.87 ? C5 SAH 501 A 1 HETATM 21 C C6 SAH . . . C 2 18.521 33.203 -15.537 1 86.19 ? C6 SAH 501 A 1 HETATM 22 N N6 SAH . . . C 2 17.212 33.199 -15.303 1 91.66 ? N6 SAH 501 A 1 HETATM 23 N N1 SAH . . . C 2 19.193 34.396 -15.711 1 82.01 ? N1 SAH 501 A 1 HETATM 24 C C2 SAH . . . C 2 20.552 34.39 -15.953 1 74.19 ? C2 SAH 501 A 1 HETATM 25 N N3 SAH . . . C 2 21.243 33.197 -16.022 1 64.1 ? N3 SAH 501 A 1 HETATM 26 C C4 SAH . . . C 2 20.589 32.022 -15.853 1 74.17 ? C4 SAH 501 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 26 #