data_6KDL # _model_server_result.job_id xpv6_CipVElzIhDphrOtBg _model_server_result.datetime_utc '2025-01-15 18:58:22' _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 6kdl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":901}' # _entry.id 6KDL # _exptl.entry_id 6KDL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 3 _entity.src_method nat _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 120 _cell.entry_id 6KDL _cell.length_a 192.932 _cell.length_b 192.932 _cell.length_c 50.041 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KDL _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _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 ? 3 E N N ? 3 F 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 277 n n N HN1 SAH sing 278 n n N HN2 SAH sing 279 n n CA CB SAH sing 280 n n CA C SAH sing 281 n n CA HA SAH sing 282 n n CB CG SAH sing 283 n n CB HB1 SAH sing 284 n n CB HB2 SAH sing 285 n n CG SD SAH sing 286 n n CG HG1 SAH sing 287 n n CG HG2 SAH sing 288 n n SD C5' SAH sing 289 n n C O SAH doub 290 n n C OXT SAH sing 291 n n OXT HXT SAH sing 292 n n C5' C4' SAH sing 293 n n C5' "H5'1" SAH sing 294 n n C5' "H5'2" SAH sing 295 n n C4' O4' SAH sing 296 n n C4' C3' SAH sing 297 n n C4' H4' SAH sing 298 n n O4' C1' SAH sing 299 n n C3' O3' SAH sing 300 n n C3' C2' SAH sing 301 n n C3' H3' SAH sing 302 n n O3' HO3' SAH sing 303 n n C2' O2' SAH sing 304 n n C2' C1' SAH sing 305 n n C2' H2' SAH sing 306 n n O2' HO2' SAH sing 307 n n C1' N9 SAH sing 308 n n C1' H1' SAH sing 309 n n N9 C8 SAH sing 310 n y N9 C4 SAH sing 311 n y C8 N7 SAH doub 312 n y C8 H8 SAH sing 313 n n N7 C5 SAH sing 314 n y C5 C6 SAH sing 315 n y C5 C4 SAH doub 316 n y C6 N6 SAH sing 317 n n C6 N1 SAH doub 318 n y N6 HN61 SAH sing 319 n n N6 HN62 SAH sing 320 n n N1 C2 SAH sing 321 n y C2 N3 SAH doub 322 n y C2 H2 SAH sing 323 n n N3 C4 SAH sing 324 n y # _atom_sites.entry_id 6KDL _atom_sites.fract_transf_matrix[1][1] 0.005183 _atom_sites.fract_transf_matrix[1][2] 0.002993 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005985 _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] 0.019984 _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 1005 SAH SAH . F 3 SAH D 1 901 1002 SAH SAH . G 4 HOH A 1 1001 232 HOH HOH . G 4 HOH A 2 1002 80 HOH HOH . G 4 HOH A 3 1003 177 HOH HOH . G 4 HOH A 4 1004 222 HOH HOH . G 4 HOH A 5 1005 104 HOH HOH . G 4 HOH A 6 1006 144 HOH HOH . G 4 HOH A 7 1007 25 HOH HOH . G 4 HOH A 8 1008 203 HOH HOH . G 4 HOH A 9 1009 89 HOH HOH . G 4 HOH A 10 1010 84 HOH HOH . G 4 HOH A 11 1011 96 HOH HOH . G 4 HOH A 12 1012 143 HOH HOH . G 4 HOH A 13 1013 36 HOH HOH . G 4 HOH A 14 1014 103 HOH HOH . G 4 HOH A 15 1015 75 HOH HOH . G 4 HOH A 16 1016 233 HOH HOH . G 4 HOH A 17 1017 127 HOH HOH . G 4 HOH A 18 1018 87 HOH HOH . G 4 HOH A 19 1019 112 HOH HOH . G 4 HOH A 20 1020 119 HOH HOH . G 4 HOH A 21 1021 108 HOH HOH . G 4 HOH A 22 1022 120 HOH HOH . G 4 HOH A 23 1023 223 HOH HOH . G 4 HOH A 24 1024 140 HOH HOH . G 4 HOH A 25 1025 185 HOH HOH . G 4 HOH A 26 1026 125 HOH HOH . G 4 HOH A 27 1027 91 HOH HOH . G 4 HOH A 28 1028 94 HOH HOH . G 4 HOH A 29 1029 113 HOH HOH . G 4 HOH A 30 1030 105 HOH HOH . G 4 HOH A 31 1031 221 HOH HOH . G 4 HOH A 32 1032 197 HOH HOH . G 4 HOH A 33 1033 90 HOH HOH . G 4 HOH A 34 1034 88 HOH HOH . G 4 HOH A 35 1035 128 HOH HOH . G 4 HOH A 36 1036 102 HOH HOH . G 4 HOH A 37 1037 230 HOH HOH . G 4 HOH A 38 1038 86 HOH HOH . G 4 HOH A 39 1039 100 HOH HOH . G 4 HOH A 40 1040 78 HOH HOH . G 4 HOH A 41 1041 32 HOH HOH . G 4 HOH A 42 1042 81 HOH HOH . G 4 HOH A 43 1043 129 HOH HOH . G 4 HOH A 44 1044 98 HOH HOH . G 4 HOH A 45 1045 82 HOH HOH . G 4 HOH A 46 1046 34 HOH HOH . G 4 HOH A 47 1047 231 HOH HOH . G 4 HOH A 48 1048 198 HOH HOH . G 4 HOH A 49 1049 192 HOH HOH . G 4 HOH A 50 1050 99 HOH HOH . G 4 HOH A 51 1051 20 HOH HOH . G 4 HOH A 52 1052 79 HOH HOH . G 4 HOH A 53 1053 200 HOH HOH . G 4 HOH A 54 1054 71 HOH HOH . G 4 HOH A 55 1055 117 HOH HOH . G 4 HOH A 56 1056 37 HOH HOH . G 4 HOH A 57 1057 109 HOH HOH . G 4 HOH A 58 1058 74 HOH HOH . G 4 HOH A 59 1059 22 HOH HOH . G 4 HOH A 60 1060 85 HOH HOH . G 4 HOH A 61 1061 35 HOH HOH . G 4 HOH A 62 1062 196 HOH HOH . G 4 HOH A 63 1063 199 HOH HOH . G 4 HOH A 64 1064 187 HOH HOH . G 4 HOH A 65 1065 226 HOH HOH . G 4 HOH A 66 1066 33 HOH HOH . G 4 HOH A 67 1067 234 HOH HOH . G 4 HOH A 68 1068 118 HOH HOH . G 4 HOH A 69 1069 181 HOH HOH . G 4 HOH A 70 1070 106 HOH HOH . G 4 HOH A 71 1071 178 HOH HOH . G 4 HOH A 72 1072 123 HOH HOH . G 4 HOH A 73 1073 72 HOH HOH . G 4 HOH A 74 1074 114 HOH HOH . G 4 HOH A 75 1075 97 HOH HOH . G 4 HOH A 76 1076 154 HOH HOH . G 4 HOH A 77 1077 93 HOH HOH . G 4 HOH A 78 1078 193 HOH HOH . G 4 HOH A 79 1079 115 HOH HOH . G 4 HOH A 80 1080 195 HOH HOH . G 4 HOH A 81 1081 228 HOH HOH . G 4 HOH A 82 1082 229 HOH HOH . G 4 HOH A 83 1083 101 HOH HOH . G 4 HOH A 84 1084 121 HOH HOH . H 4 HOH B 1 401 131 HOH HOH . H 4 HOH B 2 402 130 HOH HOH . H 4 HOH B 3 403 141 HOH HOH . H 4 HOH B 4 404 111 HOH HOH . H 4 HOH B 5 405 135 HOH HOH . H 4 HOH B 6 406 132 HOH HOH . H 4 HOH B 7 407 134 HOH HOH . I 4 HOH C 1 401 159 HOH HOH . I 4 HOH C 2 402 6 HOH HOH . I 4 HOH C 3 403 10 HOH HOH . I 4 HOH C 4 404 218 HOH HOH . I 4 HOH C 5 405 5 HOH HOH . I 4 HOH C 6 406 8 HOH HOH . I 4 HOH C 7 407 237 HOH HOH . I 4 HOH C 8 408 2 HOH HOH . I 4 HOH C 9 409 207 HOH HOH . I 4 HOH C 10 410 145 HOH HOH . I 4 HOH C 11 411 9 HOH HOH . J 4 HOH D 1 1001 179 HOH HOH . J 4 HOH D 2 1002 215 HOH HOH . J 4 HOH D 3 1003 202 HOH HOH . J 4 HOH D 4 1004 166 HOH HOH . J 4 HOH D 5 1005 40 HOH HOH . J 4 HOH D 6 1006 61 HOH HOH . J 4 HOH D 7 1007 52 HOH HOH . J 4 HOH D 8 1008 205 HOH HOH . J 4 HOH D 9 1009 49 HOH HOH . J 4 HOH D 10 1010 214 HOH HOH . J 4 HOH D 11 1011 30 HOH HOH . J 4 HOH D 12 1012 190 HOH HOH . J 4 HOH D 13 1013 201 HOH HOH . J 4 HOH D 14 1014 189 HOH HOH . J 4 HOH D 15 1015 173 HOH HOH . J 4 HOH D 16 1016 206 HOH HOH . J 4 HOH D 17 1017 48 HOH HOH . J 4 HOH D 18 1018 54 HOH HOH . J 4 HOH D 19 1019 235 HOH HOH . J 4 HOH D 20 1020 50 HOH HOH . J 4 HOH D 21 1021 58 HOH HOH . J 4 HOH D 22 1022 23 HOH HOH . J 4 HOH D 23 1023 24 HOH HOH . J 4 HOH D 24 1024 153 HOH HOH . J 4 HOH D 25 1025 174 HOH HOH . J 4 HOH D 26 1026 67 HOH HOH . J 4 HOH D 27 1027 51 HOH HOH . J 4 HOH D 28 1028 165 HOH HOH . J 4 HOH D 29 1029 57 HOH HOH . J 4 HOH D 30 1030 53 HOH HOH . J 4 HOH D 31 1031 126 HOH HOH . J 4 HOH D 32 1032 31 HOH HOH . J 4 HOH D 33 1033 65 HOH HOH . J 4 HOH D 34 1034 122 HOH HOH . J 4 HOH D 35 1035 155 HOH HOH . J 4 HOH D 36 1036 167 HOH HOH . J 4 HOH D 37 1037 17 HOH HOH . J 4 HOH D 38 1038 13 HOH HOH . J 4 HOH D 39 1039 70 HOH HOH . J 4 HOH D 40 1040 188 HOH HOH . J 4 HOH D 41 1041 63 HOH HOH . J 4 HOH D 42 1042 147 HOH HOH . J 4 HOH D 43 1043 42 HOH HOH . J 4 HOH D 44 1044 150 HOH HOH . J 4 HOH D 45 1045 69 HOH HOH . J 4 HOH D 46 1046 41 HOH HOH . J 4 HOH D 47 1047 162 HOH HOH . J 4 HOH D 48 1048 14 HOH HOH . J 4 HOH D 49 1049 60 HOH HOH . J 4 HOH D 50 1050 21 HOH HOH . J 4 HOH D 51 1051 194 HOH HOH . J 4 HOH D 52 1052 95 HOH HOH . J 4 HOH D 53 1053 11 HOH HOH . J 4 HOH D 54 1054 148 HOH HOH . J 4 HOH D 55 1055 15 HOH HOH . J 4 HOH D 56 1056 224 HOH HOH . J 4 HOH D 57 1057 29 HOH HOH . J 4 HOH D 58 1058 64 HOH HOH . J 4 HOH D 59 1059 170 HOH HOH . J 4 HOH D 60 1060 62 HOH HOH . J 4 HOH D 61 1061 68 HOH HOH . J 4 HOH D 62 1062 236 HOH HOH . J 4 HOH D 63 1063 157 HOH HOH . J 4 HOH D 64 1064 149 HOH HOH . J 4 HOH D 65 1065 66 HOH HOH . J 4 HOH D 66 1066 18 HOH HOH . J 4 HOH D 67 1067 26 HOH HOH . J 4 HOH D 68 1068 146 HOH HOH . J 4 HOH D 69 1069 191 HOH HOH . J 4 HOH D 70 1070 210 HOH HOH . J 4 HOH D 71 1071 137 HOH HOH . J 4 HOH D 72 1072 28 HOH HOH . J 4 HOH D 73 1073 176 HOH HOH . J 4 HOH D 74 1074 39 HOH HOH . J 4 HOH D 75 1075 56 HOH HOH . J 4 HOH D 76 1076 46 HOH HOH . J 4 HOH D 77 1077 227 HOH HOH . J 4 HOH D 78 1078 171 HOH HOH . J 4 HOH D 79 1079 45 HOH HOH . J 4 HOH D 80 1080 175 HOH HOH . J 4 HOH D 81 1081 92 HOH HOH . J 4 HOH D 82 1082 211 HOH HOH . J 4 HOH D 83 1083 180 HOH HOH . J 4 HOH D 84 1084 209 HOH HOH . J 4 HOH D 85 1085 158 HOH HOH . J 4 HOH D 86 1086 55 HOH HOH . J 4 HOH D 87 1087 44 HOH HOH . J 4 HOH D 88 1088 151 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 78.486 -17.327 -4.429 1 75.84 ? N SAH 901 A 1 HETATM 2 C CA SAH . . . E 3 77.779 -16.834 -3.254 1 66.8 ? CA SAH 901 A 1 HETATM 3 C CB SAH . . . E 3 78.358 -15.497 -2.802 1 78.81 ? CB SAH 901 A 1 HETATM 4 C CG SAH . . . E 3 79.352 -14.858 -3.767 1 88.5 ? CG SAH 901 A 1 HETATM 5 S SD SAH . . . E 3 80.924 -14.356 -3.004 1 108.23 ? SD SAH 901 A 1 HETATM 6 C C SAH . . . E 3 76.283 -16.713 -3.538 1 62.4 ? C SAH 901 A 1 HETATM 7 O O SAH . . . E 3 75.582 -17.718 -3.658 1 60.98 ? O SAH 901 A 1 HETATM 8 O OXT SAH . . . E 3 75.729 -15.625 -3.659 1 55.46 ? OXT SAH 901 A 1 HETATM 9 C C5' SAH . . . E 3 80.251 -12.784 -2.422 1 91.1 ? C5' SAH 901 A 1 HETATM 10 C C4' SAH . . . E 3 80.212 -12.714 -0.906 1 77.36 ? C4' SAH 901 A 1 HETATM 11 O O4' SAH . . . E 3 81.495 -12.638 -0.332 1 72.5 ? O4' SAH 901 A 1 HETATM 12 C C3' SAH . . . E 3 79.633 -11.402 -0.414 1 78.65 ? C3' SAH 901 A 1 HETATM 13 O O3' SAH . . . E 3 78.229 -11.44 -0.329 1 85.33 ? O3' SAH 901 A 1 HETATM 14 C C2' SAH . . . E 3 80.214 -11.316 0.985 1 65.66 ? C2' SAH 901 A 1 HETATM 15 O O2' SAH . . . E 3 79.228 -11.487 1.968 1 65.15 ? O2' SAH 901 A 1 HETATM 16 C C1' SAH . . . E 3 81.282 -12.41 1.044 1 64.86 ? C1' SAH 901 A 1 HETATM 17 N N9 SAH . . . E 3 82.46 -11.954 1.815 1 59.26 ? N9 SAH 901 A 1 HETATM 18 C C8 SAH . . . E 3 83.317 -10.939 1.479 1 65.99 ? C8 SAH 901 A 1 HETATM 19 N N7 SAH . . . E 3 84.258 -10.843 2.449 1 56.73 ? N7 SAH 901 A 1 HETATM 20 C C5 SAH . . . E 3 84.007 -11.763 3.403 1 46.91 ? C5 SAH 901 A 1 HETATM 21 C C6 SAH . . . E 3 84.648 -12.074 4.591 1 48.79 ? C6 SAH 901 A 1 HETATM 22 N N6 SAH . . . E 3 85.729 -11.392 4.95 1 62.31 ? N6 SAH 901 A 1 HETATM 23 N N1 SAH . . . E 3 84.163 -13.087 5.39 1 37.29 ? N1 SAH 901 A 1 HETATM 24 C C2 SAH . . . E 3 83.04 -13.787 5.006 1 47.13 ? C2 SAH 901 A 1 HETATM 25 N N3 SAH . . . E 3 82.409 -13.467 3.822 1 62.1 ? N3 SAH 901 A 1 HETATM 26 C C4 SAH . . . E 3 82.886 -12.478 3.018 1 54.04 ? C4 SAH 901 A 1 # _model_server_stats.io_time_ms 91 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 26 #