data_1KPI # _model_server_result.job_id W70RJn-cqyUWnpeu8SAC-Q _model_server_result.datetime_utc '2025-07-28 01:35:57' _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 1kpi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":900}' # _entry.id 1KPI # _exptl.entry_id 1KPI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 4 _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 90 _cell.entry_id 1KPI _cell.length_a 106.71 _cell.length_b 106.71 _cell.length_c 227.498 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KPI _symmetry.cell_setting tetragonal _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA,PQS dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I 1 1 A,B,C,D,E,F,G,H,I 2 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' 6_555 x,-y+1/2,-z+1/4 1 0 0 0 -1 0 0 0 -1 0 53.355 56.8745 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id G _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 350 n n N HN1 SAH sing 351 n n N HN2 SAH sing 352 n n CA CB SAH sing 353 n n CA C SAH sing 354 n n CA HA SAH sing 355 n n CB CG SAH sing 356 n n CB HB1 SAH sing 357 n n CB HB2 SAH sing 358 n n CG SD SAH sing 359 n n CG HG1 SAH sing 360 n n CG HG2 SAH sing 361 n n SD C5' SAH sing 362 n n C O SAH doub 363 n n C OXT SAH sing 364 n n OXT HXT SAH sing 365 n n C5' C4' SAH sing 366 n n C5' "H5'1" SAH sing 367 n n C5' "H5'2" SAH sing 368 n n C4' O4' SAH sing 369 n n C4' C3' SAH sing 370 n n C4' H4' SAH sing 371 n n O4' C1' SAH sing 372 n n C3' O3' SAH sing 373 n n C3' C2' SAH sing 374 n n C3' H3' SAH sing 375 n n O3' HO3' SAH sing 376 n n C2' O2' SAH sing 377 n n C2' C1' SAH sing 378 n n C2' H2' SAH sing 379 n n O2' HO2' SAH sing 380 n n C1' N9 SAH sing 381 n n C1' H1' SAH sing 382 n n N9 C8 SAH sing 383 n y N9 C4 SAH sing 384 n y C8 N7 SAH doub 385 n y C8 H8 SAH sing 386 n n N7 C5 SAH sing 387 n y C5 C6 SAH sing 388 n y C5 C4 SAH doub 389 n y C6 N6 SAH sing 390 n n C6 N1 SAH doub 391 n y N6 HN61 SAH sing 392 n n N6 HN62 SAH sing 393 n n N1 C2 SAH sing 394 n y C2 N3 SAH doub 395 n y C2 H2 SAH sing 396 n n N3 C4 SAH sing 397 n y # _atom_sites.entry_id 1KPI _atom_sites.fract_transf_matrix[1][1] 0.009371 _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] 0.009371 _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] 0.004396 _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 B 2 CO3 A 1 902 902 CO3 CO3 . C 3 SO4 A 1 903 903 SO4 SO4 . D 3 SO4 A 1 904 904 SO4 SO4 . E 3 SO4 A 1 905 905 SO4 SO4 . F 3 SO4 A 1 906 906 SO4 SO4 . G 4 SAH A 1 900 900 SAH SAH . H 5 10A A 1 901 901 10A 10A . I 6 HOH A 1 1001 1001 HOH HOH . I 6 HOH A 2 1002 1002 HOH HOH . I 6 HOH A 3 1003 1003 HOH HOH . I 6 HOH A 4 1004 1004 HOH HOH . I 6 HOH A 5 1005 1005 HOH HOH . I 6 HOH A 6 1006 1006 HOH HOH . I 6 HOH A 7 1007 1007 HOH HOH . I 6 HOH A 8 1008 1008 HOH HOH . I 6 HOH A 9 1009 1009 HOH HOH . I 6 HOH A 10 1011 1011 HOH HOH . I 6 HOH A 11 1012 1012 HOH HOH . I 6 HOH A 12 1013 1013 HOH HOH . I 6 HOH A 13 1014 1014 HOH HOH . I 6 HOH A 14 1015 1015 HOH HOH . I 6 HOH A 15 1016 1016 HOH HOH . I 6 HOH A 16 1017 1017 HOH HOH . I 6 HOH A 17 1018 1018 HOH HOH . I 6 HOH A 18 1019 1019 HOH HOH . I 6 HOH A 19 1020 1020 HOH HOH . I 6 HOH A 20 1021 1021 HOH HOH . I 6 HOH A 21 1022 1022 HOH HOH . I 6 HOH A 22 1023 1023 HOH HOH . I 6 HOH A 23 1024 1024 HOH HOH . I 6 HOH A 24 1025 1025 HOH HOH . I 6 HOH A 25 1026 1026 HOH HOH . I 6 HOH A 26 1027 1027 HOH HOH . I 6 HOH A 27 1028 1028 HOH HOH . I 6 HOH A 28 1029 1029 HOH HOH . I 6 HOH A 29 1030 1030 HOH HOH . I 6 HOH A 30 1031 1031 HOH HOH . I 6 HOH A 31 1032 1032 HOH HOH . I 6 HOH A 32 1033 1033 HOH HOH . I 6 HOH A 33 1034 1034 HOH HOH . I 6 HOH A 34 1035 1035 HOH HOH . I 6 HOH A 35 1036 1036 HOH HOH . I 6 HOH A 36 1037 1037 HOH HOH . I 6 HOH A 37 1038 1038 HOH HOH . I 6 HOH A 38 1040 1040 HOH HOH . I 6 HOH A 39 1041 1041 HOH HOH . I 6 HOH A 40 1042 1042 HOH HOH . I 6 HOH A 41 1043 1043 HOH HOH . I 6 HOH A 42 1044 1044 HOH HOH . I 6 HOH A 43 1045 1045 HOH HOH . I 6 HOH A 44 1046 1046 HOH HOH . I 6 HOH A 45 1047 1047 HOH HOH . I 6 HOH A 46 1048 1048 HOH HOH . I 6 HOH A 47 1049 1049 HOH HOH . I 6 HOH A 48 1050 1050 HOH HOH . I 6 HOH A 49 1051 1051 HOH HOH . I 6 HOH A 50 1052 1052 HOH HOH . I 6 HOH A 51 1053 1053 HOH HOH . I 6 HOH A 52 1054 1054 HOH HOH . I 6 HOH A 53 1055 1055 HOH HOH . I 6 HOH A 54 1056 1056 HOH HOH . I 6 HOH A 55 1057 1057 HOH HOH . I 6 HOH A 56 1058 1058 HOH HOH . I 6 HOH A 57 1059 1059 HOH HOH . I 6 HOH A 58 1060 1060 HOH HOH . I 6 HOH A 59 1061 1061 HOH HOH . I 6 HOH A 60 1062 1062 HOH HOH . I 6 HOH A 61 1063 1063 HOH HOH . I 6 HOH A 62 1064 1064 HOH HOH . # 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 . . . G 4 95.959 40.108 7.307 1 39.29 ? N SAH 900 A 1 HETATM 2 C CA SAH . . . G 4 96.871 39.092 6.778 1 40.55 ? CA SAH 900 A 1 HETATM 3 C CB SAH . . . G 4 97.71 38.404 7.882 1 40.01 ? CB SAH 900 A 1 HETATM 4 C CG SAH . . . G 4 97.019 38.03 9.208 1 37.62 ? CG SAH 900 A 1 HETATM 5 S SD SAH . . . G 4 98.142 37.212 10.37 1 37.87 ? SD SAH 900 A 1 HETATM 6 C C SAH . . . G 4 96.105 38.024 5.981 1 40.84 ? C SAH 900 A 1 HETATM 7 O O SAH . . . G 4 94.856 38.045 6.019 1 39.69 ? O SAH 900 A 1 HETATM 8 O OXT SAH . . . G 4 96.765 37.175 5.327 1 42.89 ? OXT SAH 900 A 1 HETATM 9 C C5' SAH . . . G 4 98.241 38.449 11.711 1 38.61 ? C5' SAH 900 A 1 HETATM 10 C C4' SAH . . . G 4 99.012 39.687 11.263 1 37.5 ? C4' SAH 900 A 1 HETATM 11 O O4' SAH . . . G 4 98.839 40.837 12.132 1 36.76 ? O4' SAH 900 A 1 HETATM 12 C C3' SAH . . . G 4 100.522 39.457 11.144 1 37.91 ? C3' SAH 900 A 1 HETATM 13 O O3' SAH . . . G 4 101 39.945 9.865 1 35.62 ? O3' SAH 900 A 1 HETATM 14 C C2' SAH . . . G 4 101.1 40.222 12.316 1 37 ? C2' SAH 900 A 1 HETATM 15 O O2' SAH . . . G 4 102.438 40.648 12.046 1 37.63 ? O2' SAH 900 A 1 HETATM 16 C C1' SAH . . . G 4 100.142 41.356 12.475 1 36.62 ? C1' SAH 900 A 1 HETATM 17 N N9 SAH . . . G 4 100.125 41.966 13.816 1 37.52 ? N9 SAH 900 A 1 HETATM 18 C C8 SAH . . . G 4 99.981 41.414 15.048 1 39.16 ? C8 SAH 900 A 1 HETATM 19 N N7 SAH . . . G 4 99.999 42.22 16.071 1 37.21 ? N7 SAH 900 A 1 HETATM 20 C C5 SAH . . . G 4 100.172 43.451 15.464 1 37.43 ? C5 SAH 900 A 1 HETATM 21 C C6 SAH . . . G 4 100.287 44.897 15.999 1 38.18 ? C6 SAH 900 A 1 HETATM 22 N N6 SAH . . . G 4 100.223 45.207 17.309 1 37.64 ? N6 SAH 900 A 1 HETATM 23 N N1 SAH . . . G 4 100.456 45.882 15.061 1 38.02 ? N1 SAH 900 A 1 HETATM 24 C C2 SAH . . . G 4 100.517 45.553 13.738 1 36.39 ? C2 SAH 900 A 1 HETATM 25 N N3 SAH . . . G 4 100.431 44.334 13.155 1 36.36 ? N3 SAH 900 A 1 HETATM 26 C C4 SAH . . . G 4 100.257 43.32 14.083 1 38.23 ? C4 SAH 900 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 26 #