0.023794 0.000000 0.004655 0.000000 0.019044 0.000000 0.000000 0.000000 0.019184 0.00000 0.00000 0.00000 Page, R.C. Pruneda, J.N. Klevit, R.E. Misra, S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 2 90.00 101.07 90.00 42.027 52.510 53.114 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C3 H8 O3 92.094 GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL non-polymer C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N N N 49 N O N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N N N 59 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N O N 66 N O N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N N N 75 R C N 76 N C N 77 N O N 78 N C N 79 N S N 80 N O N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N N N 89 S C N 90 N C N 91 N O N 92 N C N 93 N C N 94 N C N 95 N O N 96 N N N 97 N O N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N N N 109 S C N 110 N C N 111 N O N 112 N C N 113 N C N 114 N C N 115 N O N 116 N O N 117 N O N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N N N 128 N C N 129 N C N 130 N O N 131 N O N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N C N 138 N O N 139 N C N 140 N O N 141 N C N 142 N O N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N N N 152 S C N 153 N C N 154 N O N 155 N C Y 156 N C Y 157 N N Y 158 N C Y 159 N C Y 160 N N N 161 N O N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N O N 173 N H N 174 N H N 175 N N N 176 S C N 177 N C N 178 N O N 179 S C N 180 N C N 181 N C N 182 N C N 183 N O N 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N N N 198 S C N 199 N C N 200 N O N 201 N C N 202 N C N 203 N C N 204 N C N 205 N O N 206 N H N 207 N H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N N N 220 S C N 221 N C N 222 N O N 223 N C N 224 N C N 225 N C N 226 N C N 227 N N N 228 N O N 229 N H N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N H N 238 N H N 239 N H N 240 N H N 241 N H N 242 N H N 243 N H N 244 N N N 245 S C N 246 N C N 247 N O N 248 N C N 249 N C N 250 N S N 251 N C N 252 N O N 253 N H N 254 N H N 255 N H N 256 N H N 257 N H N 258 N H N 259 N H N 260 N H N 261 N H N 262 N H N 263 N H N 264 N N N 265 S C N 266 N C N 267 N O N 268 N C Y 269 N C Y 270 N C Y 271 N C Y 272 N C Y 273 N C Y 274 N C N 275 N O N 276 N H N 277 N H N 278 N H N 279 N H N 280 N H N 281 N H N 282 N H N 283 N H N 284 N H N 285 N H N 286 N H N 287 N N N 288 S C N 289 N C N 290 N O N 291 N C N 292 N C N 293 N C N 294 N O N 295 N H N 296 N H N 297 N H N 298 N H N 299 N H N 300 N H N 301 N H N 302 N H N 303 N H N 304 N N N 305 S C N 306 N C N 307 N O N 308 N C N 309 N O N 310 N O N 311 N H N 312 N H N 313 N H N 314 N H N 315 N H N 316 N H N 317 N H N 318 N N N 319 S C N 320 N C N 321 N O N 322 R C N 323 N O N 324 N C N 325 N O N 326 N H N 327 N H N 328 N H N 329 N H N 330 N H N 331 N H N 332 N H N 333 N H N 334 N H N 335 N N N 336 S C N 337 N C N 338 N O N 339 N C Y 340 N C Y 341 N C Y 342 N C Y 343 N N Y 344 N C Y 345 N C Y 346 N C Y 347 N C Y 348 N C N 349 N O N 350 N H N 351 N H N 352 N H N 353 N H N 354 N H N 355 N H N 356 N H N 357 N H N 358 N H N 359 N H N 360 N H N 361 N H N 362 N N N 363 S C N 364 N C N 365 N O N 366 N C Y 367 N C Y 368 N C Y 369 N C Y 370 N C Y 371 N C Y 372 N C N 373 N O N 374 N O N 375 N H N 376 N H N 377 N H N 378 N H N 379 N H N 380 N H N 381 N H N 382 N H N 383 N H N 384 N H N 385 N H N 386 N N N 387 S C N 388 N C N 389 N O N 390 N C N 391 N C N 392 N C N 393 N O N 394 N H N 395 N H N 396 N H N 397 N H N 398 N H N 399 N H N 400 N H N 401 N H N 402 N H N 403 N H N 404 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N doub N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N doub N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N doub N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N doub N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N doub N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N doub N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N doub N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N doub N 149 N sing N 150 N sing N 151 N sing N 152 N sing Y 153 N sing Y 154 N doub Y 155 N doub N 156 N sing Y 157 N sing N 158 N sing Y 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N doub N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N doub N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N doub N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N doub N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N doub N 257 N sing N 258 N sing N 259 N sing N 260 N sing Y 261 N doub Y 262 N sing Y 263 N sing N 264 N sing Y 265 N doub N 266 N sing Y 267 N doub N 268 N sing Y 269 N sing N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N doub N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N sing N 289 N sing N 290 N sing N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N doub N 297 N sing N 298 N sing N 299 N sing N 300 N sing N 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N sing N 309 N doub N 310 N sing N 311 N sing N 312 N sing N 313 N sing N 314 N sing N 315 N sing N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N sing N 321 N sing N 322 N sing N 323 N sing N 324 N sing N 325 N doub N 326 N sing N 327 N sing N 328 N sing N 329 N sing Y 330 N doub Y 331 N sing Y 332 N sing N 333 N sing Y 334 N doub Y 335 N sing Y 336 N sing N 337 N sing Y 338 N sing Y 339 N doub N 340 N sing Y 341 N doub N 342 N sing Y 343 N sing N 344 N sing N 345 N sing N 346 N sing N 347 N sing N 348 N sing N 349 N sing N 350 N sing N 351 N sing N 352 N sing N 353 N doub N 354 N sing N 355 N sing N 356 N sing N 357 N sing Y 358 N doub Y 359 N sing Y 360 N sing N 361 N sing Y 362 N doub N 363 N sing Y 364 N doub N 365 N sing Y 366 N sing N 367 N sing N 368 N sing N 369 N sing N 370 N sing N 371 N sing N 372 N sing N 373 N sing N 374 N sing N 375 N sing N 376 N sing N 377 N doub N 378 N sing N 379 N sing N 380 N sing N 381 N sing N 382 N sing N 383 N sing N 384 N sing N 385 N sing N 386 N sing N 387 N sing N 388 N sing US Biochemistry BICHAW 0033 0006-2960 51 4175 4187 10.1021/bi300058m 22551455 Structural insights into the conformation and oligomerization of E2~ubiquitin conjugates. 2012 10.2210/pdb3ugb/pdb pdb_00003ugb 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 113 1 mirrors CCD 2011-08-09 RIGAKU SATURN 944+ VariMax confocal SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU MICROMAX-007 HF 16690.068 Ubiquitin-conjugating enzyme E2 D3 6.3.2.19 unp residues 1-147 C85S 1 man polymer 8576.831 Polyubiquitin-C unp residues 1-76 1 man polymer 92.094 GLYCEROL 2 syn non-polymer 18.015 water 128 nat water Ubiquitin carrier protein D3, Ubiquitin-conjugating enzyme E2(17)KB 3, Ubiquitin-conjugating enzyme E2-17 kDa 3, Ubiquitin-protein ligase D3 Ubiquitin no no MALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINS NGSISLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAM MALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINS NGSISLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAM A polypeptide(L) no no MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG B polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n human sample UBC5C, UBCH5C, UBE2D2, UBE2D3 9606 Homo sapiens 562 Escherichia coli PLASMID pET28N human sample UBC 9606 Homo sapiens 562 Escherichia coli PLASMID pET24 1 2.28 45.97 VAPOR DIFFUSION, HANGING DROP 7 0.2M tri-potassium citrate, 20% PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K 298 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_conn struct_ref_seq_dif struct_site repository Initial release Database references Data collection Database references Derived calculations Refinement description 1 0 2012-05-16 1 1 2012-11-14 1 2 2023-09-13 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id UbcH5 isoform b (UbcH5b) conjugated to ubiquitin UbcH5 isoform b (UbcH5b) conjugated to ubiquitin in complex with the NEDD4L HECT domain E2 enzyme Ubc1 conjugated to ubiquitin E2 enzyme Ubc13 conjugated to ubiquitin in complex with Mms2 E2 enzyme UbcH8 conjugated by a non-native disulfide bond to ubiquitin(Cys77) RCSB Y RCSB 2011-11-02 REL REL GOL GLYCEROL HOH water 3TGD PDB ENTRIES 3TGD AND 1UBQ PDB experimental model 1UBQ PDB ENTRIES 3TGD AND 1UBQ PDB experimental model GOL 1 3 GOL GOL 201 A GOL 2 3 GOL GOL 202 A HOH 1 4 HOH HOH 301 A HOH 2 4 HOH HOH 302 A HOH 3 4 HOH HOH 303 A HOH 4 4 HOH HOH 304 A HOH 5 4 HOH HOH 305 A HOH 6 4 HOH HOH 306 A HOH 7 4 HOH HOH 307 A HOH 8 4 HOH HOH 308 A HOH 9 4 HOH HOH 309 A HOH 10 4 HOH HOH 310 A HOH 12 4 HOH HOH 311 A HOH 13 4 HOH HOH 312 A HOH 14 4 HOH HOH 313 A HOH 15 4 HOH HOH 314 A HOH 16 4 HOH HOH 315 A HOH 22 4 HOH HOH 316 A HOH 23 4 HOH HOH 317 A HOH 24 4 HOH HOH 318 A HOH 25 4 HOH HOH 319 A HOH 26 4 HOH HOH 320 A HOH 27 4 HOH HOH 321 A HOH 28 4 HOH HOH 322 A HOH 29 4 HOH HOH 323 A HOH 34 4 HOH HOH 324 A HOH 35 4 HOH HOH 325 A HOH 37 4 HOH HOH 326 A HOH 40 4 HOH HOH 327 A HOH 41 4 HOH HOH 328 A HOH 42 4 HOH HOH 329 A HOH 43 4 HOH HOH 330 A HOH 44 4 HOH HOH 331 A HOH 45 4 HOH HOH 332 A HOH 46 4 HOH HOH 333 A HOH 47 4 HOH HOH 334 A HOH 48 4 HOH HOH 335 A HOH 49 4 HOH HOH 336 A HOH 50 4 HOH HOH 337 A HOH 53 4 HOH HOH 338 A HOH 54 4 HOH HOH 339 A HOH 55 4 HOH HOH 340 A HOH 57 4 HOH HOH 341 A HOH 59 4 HOH HOH 342 A HOH 60 4 HOH HOH 343 A HOH 61 4 HOH HOH 344 A HOH 63 4 HOH HOH 345 A HOH 66 4 HOH HOH 346 A HOH 67 4 HOH HOH 347 A HOH 68 4 HOH HOH 348 A HOH 69 4 HOH HOH 349 A HOH 70 4 HOH HOH 350 A HOH 71 4 HOH HOH 351 A HOH 72 4 HOH HOH 352 A HOH 73 4 HOH HOH 353 A HOH 75 4 HOH HOH 354 A HOH 76 4 HOH HOH 355 A HOH 77 4 HOH HOH 356 A HOH 78 4 HOH HOH 357 A HOH 79 4 HOH HOH 358 A HOH 80 4 HOH HOH 359 A HOH 81 4 HOH HOH 360 A HOH 82 4 HOH HOH 361 A HOH 83 4 HOH HOH 362 A HOH 84 4 HOH HOH 363 A HOH 85 4 HOH HOH 364 A HOH 86 4 HOH HOH 365 A HOH 87 4 HOH HOH 366 A HOH 88 4 HOH HOH 367 A HOH 89 4 HOH HOH 368 A HOH 90 4 HOH HOH 369 A HOH 91 4 HOH HOH 370 A HOH 95 4 HOH HOH 371 A HOH 101 4 HOH HOH 372 A HOH 105 4 HOH HOH 373 A HOH 107 4 HOH HOH 374 A HOH 108 4 HOH HOH 375 A HOH 109 4 HOH HOH 376 A HOH 110 4 HOH HOH 377 A HOH 111 4 HOH HOH 378 A HOH 112 4 HOH HOH 379 A HOH 113 4 HOH HOH 380 A HOH 115 4 HOH HOH 381 A HOH 116 4 HOH HOH 382 A HOH 120 4 HOH HOH 383 A HOH 121 4 HOH HOH 384 A HOH 122 4 HOH HOH 385 A HOH 124 4 HOH HOH 386 A HOH 126 4 HOH HOH 387 A HOH 127 4 HOH HOH 388 A HOH 130 4 HOH HOH 389 A HOH 131 4 HOH HOH 390 A HOH 17 4 HOH HOH 101 B HOH 18 4 HOH HOH 102 B HOH 19 4 HOH HOH 103 B HOH 20 4 HOH HOH 104 B HOH 21 4 HOH HOH 105 B HOH 30 4 HOH HOH 106 B HOH 31 4 HOH HOH 107 B HOH 32 4 HOH HOH 108 B HOH 33 4 HOH HOH 109 B HOH 36 4 HOH HOH 110 B HOH 38 4 HOH HOH 111 B HOH 39 4 HOH HOH 112 B HOH 51 4 HOH HOH 113 B HOH 52 4 HOH HOH 114 B HOH 56 4 HOH HOH 115 B HOH 58 4 HOH HOH 116 B HOH 62 4 HOH HOH 117 B HOH 64 4 HOH HOH 118 B HOH 65 4 HOH HOH 119 B HOH 74 4 HOH HOH 120 B HOH 92 4 HOH HOH 121 B HOH 96 4 HOH HOH 122 B HOH 97 4 HOH HOH 123 B HOH 98 4 HOH HOH 124 B HOH 99 4 HOH HOH 125 B HOH 100 4 HOH HOH 126 B HOH 102 4 HOH HOH 127 B HOH 103 4 HOH HOH 128 B HOH 104 4 HOH HOH 129 B HOH 106 4 HOH HOH 130 B HOH 114 4 HOH HOH 131 B HOH 117 4 HOH HOH 132 B HOH 118 4 HOH HOH 133 B HOH 119 4 HOH HOH 134 B HOH 123 4 HOH HOH 135 B HOH 125 4 HOH HOH 136 B HOH 128 4 HOH HOH 137 B HOH 129 4 HOH HOH 138 B n 1 1 A ALA 2 n 2 ALA 2 A LEU 3 n 3 LEU 3 A LYS 4 n 4 LYS 4 A ARG 5 n 5 ARG 5 A ILE 6 n 6 ILE 6 A ASN 7 n 7 ASN 7 A LYS 8 n 8 LYS 8 A GLU 9 n 9 GLU 9 A LEU 10 n 10 LEU 10 A SER 11 n 11 SER 11 A ASP 12 n 12 ASP 12 A LEU 13 n 13 LEU 13 A ALA 14 n 14 ALA 14 A ARG 15 n 15 ARG 15 A ASP 16 n 16 ASP 16 A PRO 17 n 17 PRO 17 A PRO 18 n 18 PRO 18 A ALA 19 n 19 ALA 19 A GLN 20 n 20 GLN 20 A CYS 21 n 21 CYS 21 A SER 22 n 22 SER 22 A ALA 23 n 23 ALA 23 A GLY 24 n 24 GLY 24 A PRO 25 n 25 PRO 25 A VAL 26 n 26 VAL 26 A GLY 27 n 27 GLY 27 A ASP 28 n 28 ASP 28 A ASP 29 n 29 ASP 29 A MET 30 n 30 MET 30 A PHE 31 n 31 PHE 31 A HIS 32 n 32 HIS 32 A TRP 33 n 33 TRP 33 A GLN 34 n 34 GLN 34 A ALA 35 n 35 ALA 35 A THR 36 n 36 THR 36 A ILE 37 n 37 ILE 37 A MET 38 n 38 MET 38 A GLY 39 n 39 GLY 39 A PRO 40 n 40 PRO 40 A ASN 41 n 41 ASN 41 A ASP 42 n 42 ASP 42 A SER 43 n 43 SER 43 A PRO 44 n 44 PRO 44 A TYR 45 n 45 TYR 45 A GLN 46 n 46 GLN 46 A GLY 47 n 47 GLY 47 A GLY 48 n 48 GLY 48 A VAL 49 n 49 VAL 49 A PHE 50 n 50 PHE 50 A PHE 51 n 51 PHE 51 A LEU 52 n 52 LEU 52 A THR 53 n 53 THR 53 A ILE 54 n 54 ILE 54 A HIS 55 n 55 HIS 55 A PHE 56 n 56 PHE 56 A PRO 57 n 57 PRO 57 A THR 58 n 58 THR 58 A ASP 59 n 59 ASP 59 A TYR 60 n 60 TYR 60 A PRO 61 n 61 PRO 61 A PHE 62 n 62 PHE 62 A LYS 63 n 63 LYS 63 A PRO 64 n 64 PRO 64 A PRO 65 n 65 PRO 65 A LYS 66 n 66 LYS 66 A VAL 67 n 67 VAL 67 A ALA 68 n 68 ALA 68 A PHE 69 n 69 PHE 69 A THR 70 n 70 THR 70 A THR 71 n 71 THR 71 A ARG 72 n 72 ARG 72 A ILE 73 n 73 ILE 73 A TYR 74 n 74 TYR 74 A HIS 75 n 75 HIS 75 A PRO 76 n 76 PRO 76 A ASN 77 n 77 ASN 77 A ILE 78 n 78 ILE 78 A ASN 79 n 79 ASN 79 A SER 80 n 80 SER 80 A ASN 81 n 81 ASN 81 A GLY 82 n 82 GLY 82 A SER 83 n 83 SER 83 A ILE 84 n 84 ILE 84 A SER 85 n 85 SER 85 A LEU 86 n 86 LEU 86 A ASP 87 n 87 ASP 87 A ILE 88 n 88 ILE 88 A LEU 89 n 89 LEU 89 A ARG 90 n 90 ARG 90 A SER 91 n 91 SER 91 A GLN 92 n 92 GLN 92 A TRP 93 n 93 TRP 93 A SER 94 n 94 SER 94 A PRO 95 n 95 PRO 95 A ALA 96 n 96 ALA 96 A LEU 97 n 97 LEU 97 A THR 98 n 98 THR 98 A ILE 99 n 99 ILE 99 A SER 100 n 100 SER 100 A LYS 101 n 101 LYS 101 A VAL 102 n 102 VAL 102 A LEU 103 n 103 LEU 103 A LEU 104 n 104 LEU 104 A SER 105 n 105 SER 105 A ILE 106 n 106 ILE 106 A CYS 107 n 107 CYS 107 A SER 108 n 108 SER 108 A LEU 109 n 109 LEU 109 A LEU 110 n 110 LEU 110 A CYS 111 n 111 CYS 111 A ASP 112 n 112 ASP 112 A PRO 113 n 113 PRO 113 A ASN 114 n 114 ASN 114 A PRO 115 n 115 PRO 115 A ASP 116 n 116 ASP 116 A ASP 117 n 117 ASP 117 A PRO 118 n 118 PRO 118 A LEU 119 n 119 LEU 119 A VAL 120 n 120 VAL 120 A PRO 121 n 121 PRO 121 A GLU 122 n 122 GLU 122 A ILE 123 n 123 ILE 123 A ALA 124 n 124 ALA 124 A ARG 125 n 125 ARG 125 A ILE 126 n 126 ILE 126 A TYR 127 n 127 TYR 127 A LYS 128 n 128 LYS 128 A THR 129 n 129 THR 129 A ASP 130 n 130 ASP 130 A ARG 131 n 131 ARG 131 A ASP 132 n 132 ASP 132 A LYS 133 n 133 LYS 133 A TYR 134 n 134 TYR 134 A ASN 135 n 135 ASN 135 A ARG 136 n 136 ARG 136 A ILE 137 n 137 ILE 137 A SER 138 n 138 SER 138 A ARG 139 n 139 ARG 139 A GLU 140 n 140 GLU 140 A TRP 141 n 141 TRP 141 A THR 142 n 142 THR 142 A GLN 143 n 143 GLN 143 A LYS 144 n 144 LYS 144 A TYR 145 n 145 TYR 145 A ALA 146 n 146 ALA 146 A MET 147 n 147 MET 147 A MET 1 n 1 MET 1 B GLN 2 n 2 GLN 2 B ILE 3 n 3 ILE 3 B PHE 4 n 4 PHE 4 B VAL 5 n 5 VAL 5 B LYS 6 n 6 LYS 6 B THR 7 n 7 THR 7 B LEU 8 n 8 LEU 8 B THR 9 n 9 THR 9 B GLY 10 n 10 GLY 10 B LYS 11 n 11 LYS 11 B THR 12 n 12 THR 12 B ILE 13 n 13 ILE 13 B THR 14 n 14 THR 14 B LEU 15 n 15 LEU 15 B GLU 16 n 16 GLU 16 B VAL 17 n 17 VAL 17 B GLU 18 n 18 GLU 18 B PRO 19 n 19 PRO 19 B SER 20 n 20 SER 20 B ASP 21 n 21 ASP 21 B THR 22 n 22 THR 22 B ILE 23 n 23 ILE 23 B GLU 24 n 24 GLU 24 B ASN 25 n 25 ASN 25 B VAL 26 n 26 VAL 26 B LYS 27 n 27 LYS 27 B ALA 28 n 28 ALA 28 B LYS 29 n 29 LYS 29 B ILE 30 n 30 ILE 30 B GLN 31 n 31 GLN 31 B ASP 32 n 32 ASP 32 B LYS 33 n 33 LYS 33 B GLU 34 n 34 GLU 34 B GLY 35 n 35 GLY 35 B ILE 36 n 36 ILE 36 B PRO 37 n 37 PRO 37 B PRO 38 n 38 PRO 38 B ASP 39 n 39 ASP 39 B GLN 40 n 40 GLN 40 B GLN 41 n 41 GLN 41 B ARG 42 n 42 ARG 42 B LEU 43 n 43 LEU 43 B ILE 44 n 44 ILE 44 B PHE 45 n 45 PHE 45 B ALA 46 n 46 ALA 46 B GLY 47 n 47 GLY 47 B LYS 48 n 48 LYS 48 B GLN 49 n 49 GLN 49 B LEU 50 n 50 LEU 50 B GLU 51 n 51 GLU 51 B ASP 52 n 52 ASP 52 B GLY 53 n 53 GLY 53 B ARG 54 n 54 ARG 54 B THR 55 n 55 THR 55 B LEU 56 n 56 LEU 56 B SER 57 n 57 SER 57 B ASP 58 n 58 ASP 58 B TYR 59 n 59 TYR 59 B ASN 60 n 60 ASN 60 B ILE 61 n 61 ILE 61 B GLN 62 n 62 GLN 62 B LYS 63 n 63 LYS 63 B GLU 64 n 64 GLU 64 B SER 65 n 65 SER 65 B THR 66 n 66 THR 66 B LEU 67 n 67 LEU 67 B HIS 68 n 68 HIS 68 B LEU 69 n 69 LEU 69 B VAL 70 n 70 VAL 70 B LEU 71 n 71 LEU 71 B ARG 72 n 72 ARG 72 B LEU 73 n 73 LEU 73 B ARG 74 n 74 ARG 74 B GLY 75 n 75 GLY 75 B GLY 76 n 76 GLY 76 B 6.5471 3.2338 0.9008 3.9464 -0.0440 4.4650 -0.0814 -0.0414 -1.0833 -0.3197 0.0609 -0.8688 0.2180 0.6901 0.1054 0.1840 0.0234 0.0034 0.3693 0.0303 0.3211 refined 7.2229 -0.8634 -35.8991 X-RAY DIFFRACTION 3.7968 2.8299 -1.2038 3.4229 -0.2780 2.2792 -0.0827 0.3466 -0.1317 -0.3985 0.0010 -0.1624 -0.0015 -0.0194 0.1016 0.1072 0.0813 -0.0134 0.2544 -0.0038 0.1396 refined -2.9581 0.8857 -32.5569 X-RAY DIFFRACTION 3.7544 0.5645 -2.2327 5.9118 -3.0206 7.1510 0.3975 0.2436 0.3276 0.0273 -0.2922 0.4697 -0.2389 -0.1844 -0.1135 0.0896 -0.0062 0.0068 0.1716 -0.0092 0.1498 refined -12.8919 0.6069 -25.6323 X-RAY DIFFRACTION 7.8437 6.6398 0.0979 6.8981 0.7890 2.0924 -0.0475 0.0034 -0.0114 0.0761 -0.3957 -0.3117 -0.2600 0.3003 0.1777 0.1341 -0.0413 -0.0820 0.2627 0.1067 0.1845 refined 0.7943 1.1390 -22.7659 X-RAY DIFFRACTION 2.2101 -0.4857 -2.2421 6.5462 -4.6476 8.5021 -0.0384 -0.2786 0.1360 0.6649 -0.0323 0.3149 -0.2812 0.1963 0.1155 0.2617 -0.0263 0.0367 0.1314 -0.0300 0.2194 refined -14.8559 -3.6068 -12.6993 X-RAY DIFFRACTION 3.0115 1.2910 0.4936 2.8398 0.8161 2.0611 -0.1264 0.3533 -0.1089 0.0486 -0.1422 0.5036 0.0681 -0.3173 -0.3188 0.1048 -0.0458 -0.0365 0.1724 -0.1249 0.4373 refined -18.8259 -11.7882 -23.4024 X-RAY DIFFRACTION 4.2478 1.1569 0.0840 5.9909 2.1733 4.3608 0.0105 -0.0368 -0.2206 -0.0273 0.0205 0.6114 0.0515 -0.6504 0.0688 0.2585 -0.0519 -0.0175 0.2702 0.0366 0.2641 refined -33.8018 8.0583 -5.8649 X-RAY DIFFRACTION 3.2583 -2.9200 -0.7350 3.1493 0.2512 3.3699 -0.0757 -0.4144 -0.0771 0.2075 0.2472 0.0296 0.1384 -0.1141 -0.0810 0.3077 -0.0653 -0.0415 0.2031 0.0002 0.1286 refined -24.4062 10.5580 -4.9984 X-RAY DIFFRACTION 2.2801 -0.5409 -0.9781 2.4725 0.0986 2.2832 -0.0512 0.2137 0.0385 0.3938 0.0637 0.3388 0.0251 -0.3491 0.0614 0.1823 -0.0797 -0.0055 0.0807 0.0332 0.0889 refined -28.2688 14.1792 -7.2435 X-RAY DIFFRACTION X-RAY DIFFRACTION 1 chain 'A' and (resseq 2:25) X-RAY DIFFRACTION 2 chain 'A' and (resseq 26:65) X-RAY DIFFRACTION 3 chain 'A' and (resseq 66:84) X-RAY DIFFRACTION 4 chain 'A' and (resseq 85:111) X-RAY DIFFRACTION 5 chain 'A' and (resseq 112:130) X-RAY DIFFRACTION 6 chain 'A' and (resseq 131:147) X-RAY DIFFRACTION 7 chain 'B' and (resseq 1:22) X-RAY DIFFRACTION 8 chain 'B' and (resseq 23:54) X-RAY DIFFRACTION 9 chain 'B' and (resseq 55:76) author_defined_assembly 4 tetrameric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 2_454 -x-1,y+1/2,-z-1 crystal symmetry operation -31.8286798368 26.2550000000 -52.1257255283 A N GLY 24 A N GLY 24 A O GLN 34 A O GLN 34 A N TRP 33 A N TRP 33 A O ILE 54 A O ILE 54 A N HIS 55 A N HIS 55 A O LYS 66 A O LYS 66 B O ILE 13 B O ILE 13 B N VAL 5 B N VAL 5 B N PHE 4 B N PHE 4 B O LEU 67 B O LEU 67 B O VAL 70 B O VAL 70 B N ARG 42 B N ARG 42 B N PHE 45 B N PHE 45 B O LYS 48 B O LYS 48 1 A MET 1 A MET 1 1 Y 1 A ARG 90 -119.42 -92.73 -3.8773 0.0000 3.1039 3.4703 0.0000 0.4070 0.2524 0.2108 0.2130 2.350 29.618 467 9298 9298 5.02 96.95 0.41 1 1.37 MOLECULAR REPLACEMENT 27.10 0.86 1.10 PDB ENTRIES 3TGD AND 1UBQ ML FLAT BULK SOLVENT MODEL 36.985 0.324 2.350 29.618 128 1907 12 0 1767 0.014 1819 1.071 2466 14.970 696 0.089 274 0.012 320 2.35 52.51 3UGB 9319 9319 0.048 1 19.2 4.89 97.1 0.204 2.35 2.43 5.0 1 3.11 78.2 data collection StructureStudio model building PHENIX (phenix 1.7.2_869) refinement PHENIX (phenix.refine: 1.7.2_869) data reduction d*TREK data scaling d*TREK phasing PHENIX 1.7.2_869 N UbcH5c~Ubiquitin Conjugate 1 N N 2 N N 3 N N 3 N N 4 N N 4 N N A ALA 2 A ALA 2 HELX_P A ASP 16 A ASP 16 1 1 15 A LEU 86 A LEU 86 HELX_P A ARG 90 A ARG 90 5 2 5 A THR 98 A THR 98 HELX_P A ASP 112 A ASP 112 1 3 15 A VAL 120 A VAL 120 HELX_P A ASP 130 A ASP 130 1 4 11 A ASP 130 A ASP 130 HELX_P A ALA 146 A ALA 146 1 5 17 B THR 22 B THR 22 HELX_P B GLY 35 B GLY 35 1 6 14 B PRO 37 B PRO 37 HELX_P B GLN 41 B GLN 41 5 7 5 covale 1.434 one A SER 85 A OG SER 85 1_555 B GLY 76 B C GLY 76 1_555 LIGASE/PROTEIN BINDING E2 ubiquitin-conjugating enzyme, ubiquitin, Ubl conjugation pathway, oxyester bond, ubiquitin-protein ligase activity, LIGASE-PROTEIN BINDING complex A TYR 60 A TYR 60 1 A PRO 61 A PRO 61 12.20 UB2D3_HUMAN UNP 1 1 P61077 MALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINS NGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAM UBC_HUMAN UNP 2 1 P0CG48 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 1 147 3UGB 1 147 P61077 A 1 1 147 1 76 3UGB 1 76 P0CG48 B 2 1 76 1 CYS engineered mutation SER 85 3UGB A P61077 UNP 85 85 4 5 anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel A CYS 21 A CYS 21 A PRO 25 A PRO 25 A HIS 32 A HIS 32 A MET 38 A MET 38 A VAL 49 A VAL 49 A HIS 55 A HIS 55 A LYS 66 A LYS 66 A PHE 69 A PHE 69 B THR 12 B THR 12 B GLU 16 B GLU 16 B GLN 2 B GLN 2 B LYS 6 B LYS 6 B THR 66 B THR 66 B VAL 70 B VAL 70 B ARG 42 B ARG 42 B PHE 45 B PHE 45 B LYS 48 B LYS 48 B GLN 49 B GLN 49 BINDING SITE FOR RESIDUE GOL A 201 A GOL 201 Software 4 BINDING SITE FOR RESIDUE GOL A 202 A GOL 202 Software 9 A HIS 55 A HIS 55 4 1_555 A PRO 57 A PRO 57 4 1_555 A THR 58 A THR 58 4 1_555 A LYS 66 A LYS 66 4 1_555 A PRO 44 A PRO 44 9 1_555 A LEU 110 A LEU 110 9 1_555 A CYS 111 A CYS 111 9 1_555 A PRO 113 A PRO 113 9 1_555 A TYR 127 A TYR 127 9 1_555 A ARG 131 A ARG 131 9 1_555 A TYR 134 A TYR 134 9 1_555 A ASN 135 A ASN 135 9 1_555 A HOH 324 E HOH 9 1_555 4 P 1 21 1