data_3CBG # _model_server_result.job_id oCgF89AqBW-BD4EoC8FzKg _model_server_result.datetime_utc '2025-03-09 04:17:18' _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 3cbg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 3CBG # _exptl.entry_id 3CBG _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 3CBG _cell.length_a 57.622 _cell.length_b 57.622 _cell.length_c 119.834 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CBG _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 4_465 y-1,x+1,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 -86.433 49.902116 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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OD1 ASP 155 A ASP 143 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc2 A OD2 ASP 181 A ASP 169 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc3 A OD1 ASN 182 A ASN 170 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc4 B MG MG . A MG 401 1_555 D O4 FER . A FER 501 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.434 ? metalc ? metalc5 B MG MG . A MG 401 1_555 E O3 4FE . A 4FE 502 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.196 ? metalc ? metalc6 B MG MG . A MG 401 1_555 E O4 4FE . A 4FE 502 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.278 ? metalc ? metalc7 B MG MG . A MG 401 1_555 F O HOH . A HOH 1128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? # _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 325 n n N HN1 SAH sing 326 n n N HN2 SAH sing 327 n n CA CB SAH sing 328 n n CA C SAH sing 329 n n CA HA SAH sing 330 n n CB CG SAH sing 331 n n CB HB1 SAH sing 332 n n CB HB2 SAH sing 333 n n CG SD SAH sing 334 n n CG HG1 SAH sing 335 n n CG HG2 SAH sing 336 n n SD C5' SAH sing 337 n n C O SAH doub 338 n n C OXT SAH sing 339 n n OXT HXT SAH sing 340 n n C5' C4' SAH sing 341 n n C5' "H5'1" SAH sing 342 n n C5' "H5'2" SAH sing 343 n n C4' O4' SAH sing 344 n n C4' C3' SAH sing 345 n n C4' H4' SAH sing 346 n n O4' C1' SAH sing 347 n n C3' O3' SAH sing 348 n n C3' C2' SAH sing 349 n n C3' H3' SAH sing 350 n n O3' HO3' SAH sing 351 n n C2' O2' SAH sing 352 n n C2' C1' SAH sing 353 n n C2' H2' SAH sing 354 n n O2' HO2' SAH sing 355 n n C1' N9 SAH sing 356 n n C1' H1' SAH sing 357 n n N9 C8 SAH sing 358 n y N9 C4 SAH sing 359 n y C8 N7 SAH doub 360 n y C8 H8 SAH sing 361 n n N7 C5 SAH sing 362 n y C5 C6 SAH sing 363 n y C5 C4 SAH doub 364 n y C6 N6 SAH sing 365 n n C6 N1 SAH doub 366 n y N6 HN61 SAH sing 367 n n N6 HN62 SAH sing 368 n n N1 C2 SAH sing 369 n y C2 N3 SAH doub 370 n y C2 H2 SAH sing 371 n n N3 C4 SAH sing 372 n y # _atom_sites.entry_id 3CBG _atom_sites.fract_transf_matrix[1][1] 0.017354 _atom_sites.fract_transf_matrix[1][2] 0.01002 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020039 _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] 0.008345 _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 MG A 1 401 401 MG MG . C 3 SAH A 1 301 301 SAH SAH . D 4 FER A 1 501 501 FER FER . E 5 4FE A 1 502 502 4FE 4FE . F 6 HOH A 1 1001 1001 HOH HOH . F 6 HOH A 2 1002 1002 HOH HOH . F 6 HOH A 3 1003 1003 HOH HOH . F 6 HOH A 4 1005 1005 HOH HOH . F 6 HOH A 5 1007 1007 HOH HOH . F 6 HOH A 6 1008 1008 HOH HOH . F 6 HOH A 7 1009 1009 HOH HOH . F 6 HOH A 8 1012 1012 HOH HOH . F 6 HOH A 9 1013 1013 HOH HOH . F 6 HOH A 10 1014 1014 HOH HOH . F 6 HOH A 11 1015 1015 HOH HOH . F 6 HOH A 12 1016 1016 HOH HOH . F 6 HOH A 13 1018 1018 HOH HOH . F 6 HOH A 14 1021 1021 HOH HOH . F 6 HOH A 15 1022 1022 HOH HOH . F 6 HOH A 16 1023 1023 HOH HOH . F 6 HOH A 17 1024 1024 HOH HOH . F 6 HOH A 18 1025 1025 HOH HOH . F 6 HOH A 19 1027 1027 HOH HOH . F 6 HOH A 20 1030 1030 HOH HOH . F 6 HOH A 21 1032 1032 HOH HOH . F 6 HOH A 22 1033 1033 HOH HOH . F 6 HOH A 23 1042 1042 HOH HOH . F 6 HOH A 24 1045 1045 HOH HOH . F 6 HOH A 25 1048 1048 HOH HOH . F 6 HOH A 26 1050 1050 HOH HOH . F 6 HOH A 27 1051 1051 HOH HOH . F 6 HOH A 28 1056 1056 HOH HOH . F 6 HOH A 29 1057 1057 HOH HOH . F 6 HOH A 30 1061 1061 HOH HOH . F 6 HOH A 31 1063 1063 HOH HOH . F 6 HOH A 32 1065 1065 HOH HOH . F 6 HOH A 33 1067 1067 HOH HOH . F 6 HOH A 34 1068 1068 HOH HOH . F 6 HOH A 35 1079 1079 HOH HOH . F 6 HOH A 36 1081 1081 HOH HOH . F 6 HOH A 37 1084 1084 HOH HOH . F 6 HOH A 38 1101 1101 HOH HOH . F 6 HOH A 39 1114 1114 HOH HOH . F 6 HOH A 40 1116 1116 HOH HOH . F 6 HOH A 41 1118 1118 HOH HOH . F 6 HOH A 42 1127 1127 HOH HOH . F 6 HOH A 43 1128 1128 HOH HOH . F 6 HOH A 44 1129 1129 HOH HOH . F 6 HOH A 45 1130 1130 HOH HOH . F 6 HOH A 46 1132 1132 HOH HOH . F 6 HOH A 47 1135 1135 HOH HOH . F 6 HOH A 48 1137 1137 HOH HOH . F 6 HOH A 49 1138 1138 HOH HOH . F 6 HOH A 50 1139 1139 HOH HOH . F 6 HOH A 51 1140 1140 HOH HOH . F 6 HOH A 52 1141 1141 HOH HOH . F 6 HOH A 53 1142 1142 HOH HOH . F 6 HOH A 54 1143 1143 HOH HOH . F 6 HOH A 55 1144 1144 HOH HOH . F 6 HOH A 56 1146 1146 HOH HOH . F 6 HOH A 57 1148 1148 HOH HOH . F 6 HOH A 58 1149 1149 HOH HOH . F 6 HOH A 59 1150 1150 HOH HOH . F 6 HOH A 60 1151 1151 HOH HOH . F 6 HOH A 61 1152 1152 HOH HOH . F 6 HOH A 62 1153 1153 HOH HOH . F 6 HOH A 63 1154 1154 HOH HOH . F 6 HOH A 64 1155 1155 HOH HOH . F 6 HOH A 65 1156 1156 HOH HOH . F 6 HOH A 66 1157 1157 HOH HOH . F 6 HOH A 67 1158 1158 HOH HOH . F 6 HOH A 68 1160 1160 HOH HOH . F 6 HOH A 69 1161 1161 HOH HOH . F 6 HOH A 70 1162 1162 HOH HOH . F 6 HOH A 71 1163 1163 HOH HOH . F 6 HOH A 72 1165 1165 HOH HOH . F 6 HOH A 73 1166 1166 HOH HOH . F 6 HOH A 74 1167 1167 HOH HOH . F 6 HOH A 75 1169 1169 HOH HOH . F 6 HOH A 76 1173 1173 HOH HOH . F 6 HOH A 77 1174 1174 HOH HOH . F 6 HOH A 78 1175 1175 HOH HOH . F 6 HOH A 79 1176 1176 HOH HOH . F 6 HOH A 80 1177 1177 HOH HOH . F 6 HOH A 81 1178 1178 HOH HOH . F 6 HOH A 82 1179 1179 HOH HOH . F 6 HOH A 83 1180 1180 HOH HOH . F 6 HOH A 84 1181 1181 HOH HOH . F 6 HOH A 85 1184 1184 HOH HOH . F 6 HOH A 86 1185 1185 HOH HOH . F 6 HOH A 87 1186 1186 HOH HOH . F 6 HOH A 88 1187 1187 HOH HOH . F 6 HOH A 89 1188 1188 HOH HOH . F 6 HOH A 90 1190 1190 HOH HOH . F 6 HOH A 91 1192 1192 HOH HOH . F 6 HOH A 92 1193 1193 HOH HOH . F 6 HOH A 93 1194 1194 HOH HOH . F 6 HOH A 94 1195 1195 HOH HOH . F 6 HOH A 95 1196 1196 HOH HOH . F 6 HOH A 96 1198 1198 HOH HOH . F 6 HOH A 97 1199 1199 HOH HOH . F 6 HOH A 98 1200 1200 HOH HOH . F 6 HOH A 99 1204 1204 HOH HOH . F 6 HOH A 100 1205 1205 HOH HOH . F 6 HOH A 101 1206 1206 HOH HOH . F 6 HOH A 102 1207 1207 HOH HOH . F 6 HOH A 103 1208 1208 HOH HOH . F 6 HOH A 104 1209 1209 HOH HOH . F 6 HOH A 105 1210 1210 HOH HOH . F 6 HOH A 106 1211 1211 HOH HOH . F 6 HOH A 107 1212 1212 HOH HOH . F 6 HOH A 108 1213 1213 HOH HOH . F 6 HOH A 109 1243 1243 HOH HOH . F 6 HOH A 110 1244 1244 HOH HOH . F 6 HOH A 111 1245 1245 HOH HOH . F 6 HOH A 112 1246 1246 HOH HOH . F 6 HOH A 113 1247 1247 HOH HOH . F 6 HOH A 114 1248 1248 HOH HOH . F 6 HOH A 115 1249 1249 HOH HOH . F 6 HOH A 116 1250 1250 HOH HOH . F 6 HOH A 117 1251 1251 HOH HOH . F 6 HOH A 118 1252 1252 HOH HOH . F 6 HOH A 119 1255 1255 HOH HOH . F 6 HOH A 120 1256 1256 HOH HOH . F 6 HOH A 121 1257 1257 HOH HOH . F 6 HOH A 122 1258 1258 HOH HOH . F 6 HOH A 123 1259 1259 HOH HOH . F 6 HOH A 124 1260 1260 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 . . . C 3 -31.648 10.282 1.054 1 19.68 ? N SAH 301 A 1 HETATM 2 C CA SAH . . . C 3 -31.154 9.26 0.121 1 21.76 ? CA SAH 301 A 1 HETATM 3 C CB SAH . . . C 3 -31.326 7.872 0.74 1 21.78 ? CB SAH 301 A 1 HETATM 4 C CG SAH . . . C 3 -30.587 7.735 2.073 1 20.39 ? CG SAH 301 A 1 HETATM 5 S SD SAH . . . C 3 -30.635 6.012 2.685 1 20.78 ? SD SAH 301 A 1 HETATM 6 C C SAH . . . C 3 -31.963 9.309 -1.177 1 22.55 ? C SAH 301 A 1 HETATM 7 O O SAH . . . C 3 -31.345 9.11 -2.246 1 24.14 ? O SAH 301 A 1 HETATM 8 O OXT SAH . . . C 3 -33.189 9.525 -1.071 1 23.92 ? OXT SAH 301 A 1 HETATM 9 C C5' SAH . . . C 3 -30.189 6.261 4.441 1 19.68 ? C5' SAH 301 A 1 HETATM 10 C C4' SAH . . . C 3 -28.697 6.509 4.667 1 22.42 ? C4' SAH 301 A 1 HETATM 11 O O4' SAH . . . C 3 -28.453 6.692 6.069 1 23.74 ? O4' SAH 301 A 1 HETATM 12 C C3' SAH . . . C 3 -27.837 5.312 4.249 1 23.57 ? C3' SAH 301 A 1 HETATM 13 O O3' SAH . . . C 3 -27.036 5.658 3.116 1 22.68 ? O3' SAH 301 A 1 HETATM 14 C C2' SAH . . . C 3 -26.941 5.072 5.466 1 23.85 ? C2' SAH 301 A 1 HETATM 15 O O2' SAH . . . C 3 -25.589 4.89 5.036 1 22.99 ? O2' SAH 301 A 1 HETATM 16 C C1' SAH . . . C 3 -27.056 6.404 6.209 1 22.65 ? C1' SAH 301 A 1 HETATM 17 N N9 SAH . . . C 3 -26.759 6.235 7.648 1 23.23 ? N9 SAH 301 A 1 HETATM 18 C C8 SAH . . . C 3 -27.336 5.342 8.449 1 22.9 ? C8 SAH 301 A 1 HETATM 19 N N7 SAH . . . C 3 -26.914 5.523 9.698 1 23.73 ? N7 SAH 301 A 1 HETATM 20 C C5 SAH . . . C 3 -26.057 6.539 9.691 1 24.21 ? C5 SAH 301 A 1 HETATM 21 C C6 SAH . . . C 3 -25.33 7.192 10.677 1 23.28 ? C6 SAH 301 A 1 HETATM 22 N N6 SAH . . . C 3 -25.418 6.803 11.946 1 20.83 ? N6 SAH 301 A 1 HETATM 23 N N1 SAH . . . C 3 -24.553 8.227 10.327 1 23.12 ? N1 SAH 301 A 1 HETATM 24 C C2 SAH . . . C 3 -24.471 8.627 9.07 1 22.44 ? C2 SAH 301 A 1 HETATM 25 N N3 SAH . . . C 3 -25.15 8.03 8.106 1 22.39 ? N3 SAH 301 A 1 HETATM 26 C C4 SAH . . . C 3 -25.949 6.991 8.383 1 23.43 ? C4 SAH 301 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 26 #