data_6KDT # _model_server_result.job_id zM9SD1sAhlQHXsXyC6RPRQ _model_server_result.datetime_utc '2024-11-25 21:58:16' _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 6kdt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":901}' # _entry.id 6KDT # _exptl.entry_id 6KDT _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 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 6KDT _cell.length_a 60.35 _cell.length_b 240.784 _cell.length_c 232.131 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KDT _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall 'C 2c 2' _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? tetrameric 4 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # 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,J,K,L 1 1 A,B,E,F,I,J 2 1 C,D,G,H,K,L 3 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 ? 3 E N N ? 3 G 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 281 n n N HN1 SAH sing 282 n n N HN2 SAH sing 283 n n CA CB SAH sing 284 n n CA C SAH sing 285 n n CA HA SAH sing 286 n n CB CG SAH sing 287 n n CB HB1 SAH sing 288 n n CB HB2 SAH sing 289 n n CG SD SAH sing 290 n n CG HG1 SAH sing 291 n n CG HG2 SAH sing 292 n n SD C5' SAH sing 293 n n C O SAH doub 294 n n C OXT SAH sing 295 n n OXT HXT SAH sing 296 n n C5' C4' SAH sing 297 n n C5' "H5'1" SAH sing 298 n n C5' "H5'2" SAH sing 299 n n C4' O4' SAH sing 300 n n C4' C3' SAH sing 301 n n C4' H4' SAH sing 302 n n O4' C1' SAH sing 303 n n C3' O3' SAH sing 304 n n C3' C2' SAH sing 305 n n C3' H3' SAH sing 306 n n O3' HO3' SAH sing 307 n n C2' O2' SAH sing 308 n n C2' C1' SAH sing 309 n n C2' H2' SAH sing 310 n n O2' HO2' SAH sing 311 n n C1' N9 SAH sing 312 n n C1' H1' SAH sing 313 n n N9 C8 SAH sing 314 n y N9 C4 SAH sing 315 n y C8 N7 SAH doub 316 n y C8 H8 SAH sing 317 n n N7 C5 SAH sing 318 n y C5 C6 SAH sing 319 n y C5 C4 SAH doub 320 n y C6 N6 SAH sing 321 n n C6 N1 SAH doub 322 n y N6 HN61 SAH sing 323 n n N6 HN62 SAH sing 324 n n N1 C2 SAH sing 325 n y C2 N3 SAH doub 326 n y C2 H2 SAH sing 327 n n N3 C4 SAH sing 328 n y # _atom_sites.entry_id 6KDT _atom_sites.fract_transf_matrix[1][1] 0.01657 _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] 0.004153 _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] 0.004308 _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 E 3 SAH A 1 901 900 SAH SAH . F 4 FMT A 1 902 2 FMT FMT . G 3 SAH D 1 901 900 SAH SAH . H 4 FMT D 1 902 1 FMT FMT . I 5 HOH A 1 1001 182 HOH HOH . I 5 HOH A 2 1002 171 HOH HOH . I 5 HOH A 3 1003 162 HOH HOH . I 5 HOH A 4 1004 54 HOH HOH . I 5 HOH A 5 1005 38 HOH HOH . I 5 HOH A 6 1006 59 HOH HOH . I 5 HOH A 7 1007 51 HOH HOH . I 5 HOH A 8 1008 56 HOH HOH . I 5 HOH A 9 1009 5 HOH HOH . I 5 HOH A 10 1010 55 HOH HOH . I 5 HOH A 11 1011 42 HOH HOH . I 5 HOH A 12 1012 163 HOH HOH . I 5 HOH A 13 1013 12 HOH HOH . I 5 HOH A 14 1014 32 HOH HOH . I 5 HOH A 15 1015 52 HOH HOH . I 5 HOH A 16 1016 36 HOH HOH . I 5 HOH A 17 1017 166 HOH HOH . I 5 HOH A 18 1018 49 HOH HOH . I 5 HOH A 19 1019 16 HOH HOH . I 5 HOH A 20 1020 22 HOH HOH . I 5 HOH A 21 1021 27 HOH HOH . I 5 HOH A 22 1022 159 HOH HOH . I 5 HOH A 23 1023 14 HOH HOH . I 5 HOH A 24 1024 19 HOH HOH . I 5 HOH A 25 1025 21 HOH HOH . I 5 HOH A 26 1026 44 HOH HOH . I 5 HOH A 27 1027 174 HOH HOH . I 5 HOH A 28 1028 58 HOH HOH . I 5 HOH A 29 1029 170 HOH HOH . I 5 HOH A 30 1030 4 HOH HOH . I 5 HOH A 31 1031 13 HOH HOH . I 5 HOH A 32 1032 48 HOH HOH . I 5 HOH A 33 1033 155 HOH HOH . I 5 HOH A 34 1034 7 HOH HOH . I 5 HOH A 35 1035 172 HOH HOH . I 5 HOH A 36 1036 18 HOH HOH . I 5 HOH A 37 1037 41 HOH HOH . I 5 HOH A 38 1038 50 HOH HOH . I 5 HOH A 39 1039 140 HOH HOH . I 5 HOH A 40 1040 153 HOH HOH . I 5 HOH A 41 1041 31 HOH HOH . I 5 HOH A 42 1042 43 HOH HOH . I 5 HOH A 43 1043 157 HOH HOH . I 5 HOH A 44 1044 158 HOH HOH . I 5 HOH A 45 1045 20 HOH HOH . I 5 HOH A 46 1046 17 HOH HOH . I 5 HOH A 47 1047 57 HOH HOH . I 5 HOH A 48 1048 180 HOH HOH . I 5 HOH A 49 1049 185 HOH HOH . I 5 HOH A 50 1050 45 HOH HOH . I 5 HOH A 51 1051 23 HOH HOH . I 5 HOH A 52 1052 11 HOH HOH . I 5 HOH A 53 1053 8 HOH HOH . I 5 HOH A 54 1054 154 HOH HOH . I 5 HOH A 55 1055 142 HOH HOH . I 5 HOH A 56 1056 26 HOH HOH . J 5 HOH B 1 401 169 HOH HOH . J 5 HOH B 2 402 66 HOH HOH . J 5 HOH B 3 403 186 HOH HOH . J 5 HOH B 4 404 10 HOH HOH . J 5 HOH B 5 405 173 HOH HOH . J 5 HOH B 6 406 161 HOH HOH . J 5 HOH B 7 407 160 HOH HOH . J 5 HOH B 8 408 60 HOH HOH . J 5 HOH B 9 409 3 HOH HOH . J 5 HOH B 10 410 63 HOH HOH . J 5 HOH B 11 411 175 HOH HOH . J 5 HOH B 12 412 65 HOH HOH . J 5 HOH B 13 413 64 HOH HOH . J 5 HOH B 14 414 46 HOH HOH . J 5 HOH B 15 415 61 HOH HOH . K 5 HOH C 1 401 183 HOH HOH . K 5 HOH C 2 402 78 HOH HOH . K 5 HOH C 3 403 188 HOH HOH . K 5 HOH C 4 404 92 HOH HOH . K 5 HOH C 5 405 90 HOH HOH . K 5 HOH C 6 406 81 HOH HOH . K 5 HOH C 7 407 80 HOH HOH . K 5 HOH C 8 408 71 HOH HOH . K 5 HOH C 9 409 76 HOH HOH . K 5 HOH C 10 410 84 HOH HOH . K 5 HOH C 11 411 77 HOH HOH . K 5 HOH C 12 412 67 HOH HOH . K 5 HOH C 13 413 150 HOH HOH . K 5 HOH C 14 414 94 HOH HOH . K 5 HOH C 15 415 86 HOH HOH . K 5 HOH C 16 416 89 HOH HOH . K 5 HOH C 17 417 144 HOH HOH . K 5 HOH C 18 418 87 HOH HOH . K 5 HOH C 19 419 88 HOH HOH . K 5 HOH C 20 420 85 HOH HOH . K 5 HOH C 21 421 143 HOH HOH . K 5 HOH C 22 422 95 HOH HOH . K 5 HOH C 23 423 93 HOH HOH . K 5 HOH C 24 424 176 HOH HOH . K 5 HOH C 25 425 151 HOH HOH . K 5 HOH C 26 426 15 HOH HOH . K 5 HOH C 27 427 69 HOH HOH . K 5 HOH C 28 428 152 HOH HOH . L 5 HOH D 1 1001 168 HOH HOH . L 5 HOH D 2 1002 134 HOH HOH . L 5 HOH D 3 1003 189 HOH HOH . L 5 HOH D 4 1004 102 HOH HOH . L 5 HOH D 5 1005 116 HOH HOH . L 5 HOH D 6 1006 133 HOH HOH . L 5 HOH D 7 1007 124 HOH HOH . L 5 HOH D 8 1008 30 HOH HOH . L 5 HOH D 9 1009 177 HOH HOH . L 5 HOH D 10 1010 117 HOH HOH . L 5 HOH D 11 1011 104 HOH HOH . L 5 HOH D 12 1012 119 HOH HOH . L 5 HOH D 13 1013 120 HOH HOH . L 5 HOH D 14 1014 167 HOH HOH . L 5 HOH D 15 1015 139 HOH HOH . L 5 HOH D 16 1016 191 HOH HOH . L 5 HOH D 17 1017 178 HOH HOH . L 5 HOH D 18 1018 105 HOH HOH . L 5 HOH D 19 1019 131 HOH HOH . L 5 HOH D 20 1020 29 HOH HOH . L 5 HOH D 21 1021 97 HOH HOH . L 5 HOH D 22 1022 98 HOH HOH . L 5 HOH D 23 1023 128 HOH HOH . L 5 HOH D 24 1024 72 HOH HOH . L 5 HOH D 25 1025 127 HOH HOH . L 5 HOH D 26 1026 99 HOH HOH . L 5 HOH D 27 1027 107 HOH HOH . L 5 HOH D 28 1028 35 HOH HOH . L 5 HOH D 29 1029 114 HOH HOH . L 5 HOH D 30 1030 121 HOH HOH . L 5 HOH D 31 1031 179 HOH HOH . L 5 HOH D 32 1032 130 HOH HOH . L 5 HOH D 33 1033 28 HOH HOH . L 5 HOH D 34 1034 106 HOH HOH . L 5 HOH D 35 1035 83 HOH HOH . L 5 HOH D 36 1036 145 HOH HOH . L 5 HOH D 37 1037 184 HOH HOH . L 5 HOH D 38 1038 34 HOH HOH . L 5 HOH D 39 1039 123 HOH HOH . L 5 HOH D 40 1040 146 HOH HOH . L 5 HOH D 41 1041 122 HOH HOH . L 5 HOH D 42 1042 190 HOH HOH . L 5 HOH D 43 1043 129 HOH HOH . L 5 HOH D 44 1044 118 HOH HOH . L 5 HOH D 45 1045 115 HOH HOH . L 5 HOH D 46 1046 109 HOH HOH . L 5 HOH D 47 1047 147 HOH HOH . L 5 HOH D 48 1048 110 HOH HOH . L 5 HOH D 49 1049 148 HOH HOH . L 5 HOH D 50 1050 187 HOH HOH . L 5 HOH D 51 1051 74 HOH HOH . L 5 HOH D 52 1052 75 HOH HOH . L 5 HOH D 53 1053 156 HOH HOH . L 5 HOH D 54 1054 149 HOH HOH . L 5 HOH D 55 1055 100 HOH HOH . L 5 HOH D 56 1056 136 HOH HOH . L 5 HOH D 57 1057 112 HOH HOH . L 5 HOH D 58 1058 135 HOH HOH . L 5 HOH D 59 1059 25 HOH HOH . L 5 HOH D 60 1060 113 HOH HOH . L 5 HOH D 61 1061 101 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 . . . E 3 -16.635 22.082 -23.548 1 58.72 ? N SAH 901 A 1 HETATM 2 C CA SAH . . . E 3 -17.292 20.91 -24.134 1 59.73 ? CA SAH 901 A 1 HETATM 3 C CB SAH . . . E 3 -16.762 20.761 -25.574 1 60.05 ? CB SAH 901 A 1 HETATM 4 C CG SAH . . . E 3 -16.067 21.973 -26.209 1 60.12 ? CG SAH 901 A 1 HETATM 5 S SD SAH . . . E 3 -15.442 21.72 -27.906 1 64.23 ? SD SAH 901 A 1 HETATM 6 C C SAH . . . E 3 -17.17 19.557 -23.366 1 50.51 ? C SAH 901 A 1 HETATM 7 O O SAH . . . E 3 -17.543 18.5 -23.897 1 42.72 ? O SAH 901 A 1 HETATM 8 O OXT SAH . . . E 3 -16.736 19.449 -22.214 1 39.46 ? OXT SAH 901 A 1 HETATM 9 C C5' SAH . . . E 3 -16.511 22.959 -28.674 1 68.61 ? C5' SAH 901 A 1 HETATM 10 C C4' SAH . . . E 3 -17.933 22.432 -28.931 1 73.44 ? C4' SAH 901 A 1 HETATM 11 O O4' SAH . . . E 3 -18.764 23.443 -29.47 1 69.75 ? O4' SAH 901 A 1 HETATM 12 C C3' SAH . . . E 3 -18.02 21.261 -29.902 1 76.07 ? C3' SAH 901 A 1 HETATM 13 O O3' SAH . . . E 3 -18.464 20.121 -29.198 1 75 ? O3' SAH 901 A 1 HETATM 14 C C2' SAH . . . E 3 -19.038 21.673 -30.962 1 71.98 ? C2' SAH 901 A 1 HETATM 15 O O2' SAH . . . E 3 -19.984 20.659 -31.228 1 65.66 ? O2' SAH 901 A 1 HETATM 16 C C1' SAH . . . E 3 -19.717 22.906 -30.374 1 70.96 ? C1' SAH 901 A 1 HETATM 17 N N9 SAH . . . E 3 -20.137 23.938 -31.37 1 67.72 ? N9 SAH 901 A 1 HETATM 18 C C8 SAH . . . E 3 -19.503 24.243 -32.551 1 59.5 ? C8 SAH 901 A 1 HETATM 19 N N7 SAH . . . E 3 -20.188 25.24 -33.161 1 57.25 ? N7 SAH 901 A 1 HETATM 20 C C5 SAH . . . E 3 -21.25 25.598 -32.393 1 58.21 ? C5 SAH 901 A 1 HETATM 21 C C6 SAH . . . E 3 -22.265 26.558 -32.541 1 57.89 ? C6 SAH 901 A 1 HETATM 22 N N6 SAH . . . E 3 -22.308 27.353 -33.616 1 56.33 ? N6 SAH 901 A 1 HETATM 23 N N1 SAH . . . E 3 -23.248 26.7 -31.571 1 56.91 ? N1 SAH 901 A 1 HETATM 24 C C2 SAH . . . E 3 -23.216 25.886 -30.462 1 55.74 ? C2 SAH 901 A 1 HETATM 25 N N3 SAH . . . E 3 -22.208 24.943 -30.326 1 59.28 ? N3 SAH 901 A 1 HETATM 26 C C4 SAH . . . E 3 -21.235 24.786 -31.267 1 63.4 ? C4 SAH 901 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 26 #