0.008383 0.004840 0.000000 0.000000 0.009680 0.000000 0.000000 0.000000 0.020077 0.00000 0.00000 0.00000 Stogios, P.J. Quaile, A.T. Skarina, T. Nocek, B. Di Leo, R. Yim, V. Savchenko, A. Joachimiak, A. Midwest Center for Structural Genomics (MCSG) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 119.293 119.293 49.809 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 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 C5 H11 N O2 Se 196.106 n SELENOMETHIONINE 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 N N 138 S C N 139 N C N 140 N O N 141 N C Y 142 N C Y 143 N N Y 144 N C Y 145 N C Y 146 N N N 147 N O N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N O N 159 N H N 160 N H N 161 N N N 162 S C N 163 N C N 164 N O N 165 S C N 166 N C N 167 N C N 168 N C N 169 N O N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N N N 184 S C N 185 N C N 186 N O N 187 N C N 188 N C N 189 N C N 190 N C N 191 N O N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H N 205 N N N 206 S C N 207 N C N 208 N O N 209 N C N 210 N C N 211 N C N 212 N C N 213 N N N 214 N O N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N H N 225 N H N 226 N H N 227 N H N 228 N H N 229 N H N 230 N N N 231 S C N 232 N C N 233 N O N 234 N C N 235 N C N 236 N S N 237 N C N 238 N O N 239 N H N 240 N H N 241 N H N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N H N 248 N H N 249 N H N 250 N N N 251 S C N 252 N C N 253 N O N 254 N O N 255 N C N 256 N C N 257 N SE N 258 N C N 259 N H N 260 N H N 261 N H N 262 N H N 263 N H N 264 N H N 265 N H N 266 N H N 267 N H N 268 N H N 269 N H N 270 N N N 271 S C N 272 N C N 273 N O N 274 N C Y 275 N C Y 276 N C Y 277 N C Y 278 N C Y 279 N C Y 280 N C N 281 N O N 282 N H N 283 N H N 284 N H N 285 N H N 286 N H N 287 N H N 288 N H N 289 N H N 290 N H N 291 N H N 292 N H N 293 N N N 294 S C N 295 N C N 296 N O N 297 N C N 298 N C N 299 N C N 300 N O N 301 N H N 302 N H N 303 N H N 304 N H N 305 N H N 306 N H N 307 N H N 308 N H N 309 N H N 310 N N N 311 S C N 312 N C N 313 N O N 314 N C N 315 N O N 316 N O N 317 N H N 318 N H N 319 N H N 320 N H N 321 N H N 322 N H N 323 N H N 324 N N N 325 S C N 326 N C N 327 N O N 328 R C N 329 N O N 330 N C N 331 N O N 332 N H N 333 N H N 334 N H N 335 N H N 336 N H N 337 N H N 338 N H N 339 N H N 340 N H N 341 N N N 342 S C N 343 N C N 344 N O N 345 N C Y 346 N C Y 347 N C Y 348 N C Y 349 N N Y 350 N C Y 351 N C Y 352 N C Y 353 N C Y 354 N C N 355 N O 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 H N 363 N H N 364 N H N 365 N H N 366 N H N 367 N H N 368 N N N 369 S C N 370 N C N 371 N O N 372 N C Y 373 N C Y 374 N C Y 375 N C Y 376 N C Y 377 N C Y 378 N C N 379 N O N 380 N O N 381 N H N 382 N H N 383 N H N 384 N H N 385 N H N 386 N H N 387 N H N 388 N H N 389 N H N 390 N H N 391 N H N 392 N N N 393 S C N 394 N C N 395 N O N 396 N C N 397 N C N 398 N C N 399 N O N 400 N H N 401 N H N 402 N H N 403 N H N 404 N H N 405 N H N 406 N H N 407 N H N 408 N H N 409 N H N 410 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 doub N 136 N sing N 137 N sing N 138 N sing N 139 N sing Y 140 N sing Y 141 N doub Y 142 N doub N 143 N sing Y 144 N sing N 145 N sing Y 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N doub N 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 sing 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 doub 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 sing 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 doub 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 sing 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 doub 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 sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N doub 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 sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N doub N 263 N sing N 264 N sing N 265 N sing N 266 N sing Y 267 N doub Y 268 N sing Y 269 N sing N 270 N sing Y 271 N doub N 272 N sing Y 273 N doub N 274 N sing Y 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N sing N 285 N doub 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 sing N 297 N sing N 298 N sing N 299 N sing N 300 N sing N 301 N sing N 302 N doub 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 sing N 310 N sing N 311 N sing N 312 N sing N 313 N sing N 314 N sing N 315 N doub 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 sing N 326 N sing N 327 N sing N 328 N sing N 329 N sing N 330 N sing N 331 N doub N 332 N sing N 333 N sing N 334 N sing N 335 N sing Y 336 N doub Y 337 N sing Y 338 N sing N 339 N sing Y 340 N doub Y 341 N sing Y 342 N sing N 343 N sing Y 344 N sing Y 345 N doub N 346 N sing Y 347 N doub N 348 N sing Y 349 N sing N 350 N sing N 351 N sing N 352 N sing N 353 N sing N 354 N sing N 355 N sing N 356 N sing N 357 N sing N 358 N sing N 359 N doub N 360 N sing N 361 N sing N 362 N sing N 363 N sing Y 364 N doub Y 365 N sing Y 366 N sing N 367 N sing Y 368 N doub N 369 N sing Y 370 N doub N 371 N sing Y 372 N sing N 373 N sing N 374 N sing N 375 N sing N 376 N sing N 377 N sing N 378 N sing N 379 N sing N 380 N sing N 381 N sing N 382 N sing N 383 N doub N 384 N sing N 385 N sing N 386 N sing N 387 N sing N 388 N sing N 389 N sing N 390 N sing N 391 N sing N 392 N sing N 393 N sing N 394 N sing UK Structure STRUE6 2005 0969-2126 23 1459 1469 10.1016/j.str.2015.05.020 26146184 Molecular Characterization of LubX: Functional Divergence of the U-Box Fold by Legionella pneumophila. 2015 10.2210/pdb4wz3/pdb pdb_00004wz3 100 1 CCD 2013-12-02 ADSC QUANTUM 315 SINGLE WAVELENGTH M x-ray 1 0.9789897 1.0 19-ID APS 0.9789897 SYNCHROTRON APS BEAMLINE 19-ID 16796.213 Ubiquitin-conjugating enzyme E2 D2 6.3.2.19 C85S 1 man polymer 24818.092 E3 ubiquitin-protein ligase LubX 6.3.2.- 1 man polymer 18.015 water 53 nat water Ubiquitin carrier protein D2,Ubiquitin-conjugating enzyme E2(17)KB 2,Ubiquitin-conjugating enzyme E2-17 kDa 2,Ubiquitin-protein ligase D2,p53-regulated ubiquitin-conjugating enzyme 1 Legionella U-box protein no no GMALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNIN SNGSISLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM GMALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNIN SNGSISLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM A polypeptide(L) no yes (MSE)ATRNPFDIDHKSKYLREAALEANLSHPETTPT(MSE)LTCPIDSGFLKDPVITPEGFVYNKSSILKWLETKKEDP QSRKPLTAKDLQPFPELLIIVNRFVETQTNYEKLKNRLVQNARVAARQKEYTEIPDIFLCPISKTLIKTPVITAQGKVYD QEALSNFLIATGNKDETGKKLSIDDVVVFDELYQQIKVYNFYRKREVQKNQIQPSVSNGFGFF MATRNPFDIDHKSKYLREAALEANLSHPETTPTMLTCPIDSGFLKDPVITPEGFVYNKSSILKWLETKKEDPQSRKPLTA KDLQPFPELLIIVNRFVETQTNYEKLKNRLVQNARVAARQKEYTEIPDIFLCPISKTLIKTPVITAQGKVYDQEALSNFL IATGNKDETGKKLSIDDVVVFDELYQQIKVYNFYRKREVQKNQIQPSVSNGFGFF B MCSG-APC108251 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 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 1 148 UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B 9606 Homo sapiens 469008 Escherichia coli BL21(DE3) plasmid Biological sequence p15TV-LIC Paris sample 1 215 lubX, lpp2887 297246 Legionella pneumophila 469008 Escherichia coli BL21(DE3) plasmid Biological sequence p15TV-LIC 2.46 49.97 VAPOR DIFFUSION, HANGING DROP 8.5 15 mg/ml of E2D2.(C85S)-Ub conjugate and an equimolar concentration of LubX (1-186), 0.2 M sodium tartrate, 0.1 M Tris-Cl (pH 8.5) and 25% PEG3350 298 Midwest Center for Structural Genomics MCSG PSI:Biology pdbx_audit_support pdbx_struct_oper_list pdbx_audit_support chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model chem_comp_atom chem_comp_bond repository Initial release Derived calculations Database references Derived calculations Author supporting evidence Derived calculations Author supporting evidence Data collection Database references Refinement description Data collection 1 0 2015-01-07 1 1 2015-02-04 1 2 2015-07-29 1 3 2015-08-19 1 4 2017-09-20 1 5 2019-12-04 1 6 2023-09-27 1 7 2023-11-15 _pdbx_audit_support.funding_organization _pdbx_struct_oper_list.symmetry_operation _pdbx_audit_support.funding_organization _database_2.pdbx_DOI _database_2.pdbx_database_accession _chem_comp_atom.atom_id _chem_comp_bond.atom_id_2 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM094585 United States Department of Energy (DOE, United States) DE-AC02-06CH11357 U-box 1 U-box 2 (wild-type) U-box 2, Ile175Met mutant Y RCSB Y RCSB 2014-11-18 REL REL HOH water 4DDI 4DDI, LubX U-box 1 WT PDB code 4WZ0 PDB experimental model 4WZ0 4DDI, LubX U-box 1 WT PDB code 4WZ0 PDB experimental model HOH 40 3 HOH HOH 201 A HOH 6 3 HOH HOH 202 A HOH 12 3 HOH HOH 203 A HOH 2 3 HOH HOH 204 A HOH 66 3 HOH HOH 205 A HOH 80 3 HOH HOH 206 A HOH 82 3 HOH HOH 207 A HOH 63 3 HOH HOH 208 A HOH 58 3 HOH HOH 209 A HOH 29 3 HOH HOH 210 A HOH 22 3 HOH HOH 211 A HOH 53 3 HOH HOH 212 A HOH 103 3 HOH HOH 213 A HOH 94 3 HOH HOH 214 A HOH 8 3 HOH HOH 215 A HOH 64 3 HOH HOH 216 A HOH 20 3 HOH HOH 217 A HOH 69 3 HOH HOH 218 A HOH 75 3 HOH HOH 219 A HOH 87 3 HOH HOH 220 A HOH 68 3 HOH HOH 221 A HOH 125 3 HOH HOH 222 A HOH 76 3 HOH HOH 223 A HOH 61 3 HOH HOH 224 A HOH 31 3 HOH HOH 225 A HOH 128 3 HOH HOH 226 A HOH 115 3 HOH HOH 227 A HOH 130 3 HOH HOH 228 A HOH 70 3 HOH HOH 301 B HOH 127 3 HOH HOH 302 B HOH 24 3 HOH HOH 303 B HOH 124 3 HOH HOH 304 B HOH 18 3 HOH HOH 305 B HOH 117 3 HOH HOH 306 B HOH 105 3 HOH HOH 307 B HOH 97 3 HOH HOH 308 B HOH 98 3 HOH HOH 309 B HOH 23 3 HOH HOH 310 B HOH 14 3 HOH HOH 311 B HOH 5 3 HOH HOH 312 B HOH 13 3 HOH HOH 313 B HOH 3 3 HOH HOH 314 B HOH 71 3 HOH HOH 315 B HOH 65 3 HOH HOH 316 B HOH 48 3 HOH HOH 317 B HOH 95 3 HOH HOH 318 B HOH 67 3 HOH HOH 319 B HOH 59 3 HOH HOH 320 B HOH 25 3 HOH HOH 321 B HOH 120 3 HOH HOH 322 B HOH 129 3 HOH HOH 323 B HOH 116 3 HOH HOH 324 B HOH 113 3 HOH HOH 325 B GLY 0 n 1 GLY 0 A MET 1 n 2 MET 1 A ALA 2 n 3 ALA 2 A LEU 3 n 4 LEU 3 A LYS 4 n 5 LYS 4 A ARG 5 n 6 ARG 5 A ILE 6 n 7 ILE 6 A HIS 7 n 8 HIS 7 A LYS 8 n 9 LYS 8 A GLU 9 n 10 GLU 9 A LEU 10 n 11 LEU 10 A ASN 11 n 12 ASN 11 A ASP 12 n 13 ASP 12 A LEU 13 n 14 LEU 13 A ALA 14 n 15 ALA 14 A ARG 15 n 16 ARG 15 A ASP 16 n 17 ASP 16 A PRO 17 n 18 PRO 17 A PRO 18 n 19 PRO 18 A ALA 19 n 20 ALA 19 A GLN 20 n 21 GLN 20 A CYS 21 n 22 CYS 21 A SER 22 n 23 SER 22 A ALA 23 n 24 ALA 23 A GLY 24 n 25 GLY 24 A PRO 25 n 26 PRO 25 A VAL 26 n 27 VAL 26 A GLY 27 n 28 GLY 27 A ASP 28 n 29 ASP 28 A ASP 29 n 30 ASP 29 A MET 30 n 31 MET 30 A PHE 31 n 32 PHE 31 A HIS 32 n 33 HIS 32 A TRP 33 n 34 TRP 33 A GLN 34 n 35 GLN 34 A ALA 35 n 36 ALA 35 A THR 36 n 37 THR 36 A ILE 37 n 38 ILE 37 A MET 38 n 39 MET 38 A GLY 39 n 40 GLY 39 A PRO 40 n 41 PRO 40 A ASN 41 n 42 ASN 41 A ASP 42 n 43 ASP 42 A SER 43 n 44 SER 43 A PRO 44 n 45 PRO 44 A TYR 45 n 46 TYR 45 A GLN 46 n 47 GLN 46 A GLY 47 n 48 GLY 47 A GLY 48 n 49 GLY 48 A VAL 49 n 50 VAL 49 A PHE 50 n 51 PHE 50 A PHE 51 n 52 PHE 51 A LEU 52 n 53 LEU 52 A THR 53 n 54 THR 53 A ILE 54 n 55 ILE 54 A HIS 55 n 56 HIS 55 A PHE 56 n 57 PHE 56 A PRO 57 n 58 PRO 57 A THR 58 n 59 THR 58 A ASP 59 n 60 ASP 59 A TYR 60 n 61 TYR 60 A PRO 61 n 62 PRO 61 A PHE 62 n 63 PHE 62 A LYS 63 n 64 LYS 63 A PRO 64 n 65 PRO 64 A PRO 65 n 66 PRO 65 A LYS 66 n 67 LYS 66 A VAL 67 n 68 VAL 67 A ALA 68 n 69 ALA 68 A PHE 69 n 70 PHE 69 A THR 70 n 71 THR 70 A THR 71 n 72 THR 71 A ARG 72 n 73 ARG 72 A ILE 73 n 74 ILE 73 A TYR 74 n 75 TYR 74 A HIS 75 n 76 HIS 75 A PRO 76 n 77 PRO 76 A ASN 77 n 78 ASN 77 A ILE 78 n 79 ILE 78 A ASN 79 n 80 ASN 79 A SER 80 n 81 SER 80 A ASN 81 n 82 ASN 81 A GLY 82 n 83 GLY 82 A SER 83 n 84 SER 83 A ILE 84 n 85 ILE 84 A SER 85 n 86 SER 85 A LEU 86 n 87 LEU 86 A ASP 87 n 88 ASP 87 A ILE 88 n 89 ILE 88 A LEU 89 n 90 LEU 89 A ARG 90 n 91 ARG 90 A SER 91 n 92 SER 91 A GLN 92 n 93 GLN 92 A TRP 93 n 94 TRP 93 A SER 94 n 95 SER 94 A PRO 95 n 96 PRO 95 A ALA 96 n 97 ALA 96 A LEU 97 n 98 LEU 97 A THR 98 n 99 THR 98 A ILE 99 n 100 ILE 99 A SER 100 n 101 SER 100 A LYS 101 n 102 LYS 101 A VAL 102 n 103 VAL 102 A LEU 103 n 104 LEU 103 A LEU 104 n 105 LEU 104 A SER 105 n 106 SER 105 A ILE 106 n 107 ILE 106 A CYS 107 n 108 CYS 107 A SER 108 n 109 SER 108 A LEU 109 n 110 LEU 109 A LEU 110 n 111 LEU 110 A CYS 111 n 112 CYS 111 A ASP 112 n 113 ASP 112 A PRO 113 n 114 PRO 113 A ASN 114 n 115 ASN 114 A PRO 115 n 116 PRO 115 A ASP 116 n 117 ASP 116 A ASP 117 n 118 ASP 117 A PRO 118 n 119 PRO 118 A LEU 119 n 120 LEU 119 A VAL 120 n 121 VAL 120 A PRO 121 n 122 PRO 121 A GLU 122 n 123 GLU 122 A ILE 123 n 124 ILE 123 A ALA 124 n 125 ALA 124 A ARG 125 n 126 ARG 125 A ILE 126 n 127 ILE 126 A TYR 127 n 128 TYR 127 A LYS 128 n 129 LYS 128 A THR 129 n 130 THR 129 A ASP 130 n 131 ASP 130 A ARG 131 n 132 ARG 131 A GLU 132 n 133 GLU 132 A LYS 133 n 134 LYS 133 A TYR 134 n 135 TYR 134 A ASN 135 n 136 ASN 135 A ARG 136 n 137 ARG 136 A ILE 137 n 138 ILE 137 A ALA 138 n 139 ALA 138 A ARG 139 n 140 ARG 139 A GLU 140 n 141 GLU 140 A TRP 141 n 142 TRP 141 A THR 142 n 143 THR 142 A GLN 143 n 144 GLN 143 A LYS 144 n 145 LYS 144 A TYR 145 n 146 TYR 145 A ALA 146 n 147 ALA 146 A MET 147 n 148 MET 147 A n 1 1 B n 2 2 B n 3 3 B ARG 4 n 4 ARG 4 B ASN 5 n 5 ASN 5 B PRO 6 n 6 PRO 6 B PHE 7 n 7 PHE 7 B ASP 8 n 8 ASP 8 B ILE 9 n 9 ILE 9 B ASP 10 n 10 ASP 10 B HIS 11 n 11 HIS 11 B LYS 12 n 12 LYS 12 B SER 13 n 13 SER 13 B LYS 14 n 14 LYS 14 B TYR 15 n 15 TYR 15 B LEU 16 n 16 LEU 16 B ARG 17 n 17 ARG 17 B GLU 18 n 18 GLU 18 B ALA 19 n 19 ALA 19 B ALA 20 n 20 ALA 20 B LEU 21 n 21 LEU 21 B GLU 22 n 22 GLU 22 B ALA 23 n 23 ALA 23 B ASN 24 n 24 ASN 24 B LEU 25 n 25 LEU 25 B SER 26 n 26 SER 26 B HIS 27 n 27 HIS 27 B PRO 28 n 28 PRO 28 B GLU 29 n 29 GLU 29 B THR 30 n 30 THR 30 B THR 31 n 31 THR 31 B PRO 32 n 32 PRO 32 B THR 33 n 33 THR 33 B MSE 34 n 34 MSE 34 B LEU 35 n 35 LEU 35 B THR 36 n 36 THR 36 B CYS 37 n 37 CYS 37 B PRO 38 n 38 PRO 38 B ILE 39 n 39 ILE 39 B ASP 40 n 40 ASP 40 B SER 41 n 41 SER 41 B GLY 42 n 42 GLY 42 B PHE 43 n 43 PHE 43 B LEU 44 n 44 LEU 44 B LYS 45 n 45 LYS 45 B ASP 46 n 46 ASP 46 B PRO 47 n 47 PRO 47 B VAL 48 n 48 VAL 48 B ILE 49 n 49 ILE 49 B THR 50 n 50 THR 50 B PRO 51 n 51 PRO 51 B GLU 52 n 52 GLU 52 B GLY 53 n 53 GLY 53 B PHE 54 n 54 PHE 54 B VAL 55 n 55 VAL 55 B TYR 56 n 56 TYR 56 B ASN 57 n 57 ASN 57 B LYS 58 n 58 LYS 58 B SER 59 n 59 SER 59 B SER 60 n 60 SER 60 B ILE 61 n 61 ILE 61 B LEU 62 n 62 LEU 62 B LYS 63 n 63 LYS 63 B TRP 64 n 64 TRP 64 B LEU 65 n 65 LEU 65 B GLU 66 n 66 GLU 66 B THR 67 n 67 THR 67 B LYS 68 n 68 LYS 68 B LYS 69 n 69 LYS 69 B GLU 70 n 70 GLU 70 B ASP 71 n 71 ASP 71 B PRO 72 n 72 PRO 72 B GLN 73 n 73 GLN 73 B SER 74 n 74 SER 74 B ARG 75 n 75 ARG 75 B LYS 76 n 76 LYS 76 B PRO 77 n 77 PRO 77 B LEU 78 n 78 LEU 78 B THR 79 n 79 THR 79 B ALA 80 n 80 ALA 80 B LYS 81 n 81 LYS 81 B ASP 82 n 82 ASP 82 B LEU 83 n 83 LEU 83 B GLN 84 n 84 GLN 84 B PRO 85 n 85 PRO 85 B PHE 86 n 86 PHE 86 B PRO 87 n 87 PRO 87 B GLU 88 n 88 GLU 88 B LEU 89 n 89 LEU 89 B LEU 90 n 90 LEU 90 B ILE 91 n 91 ILE 91 B ILE 92 n 92 ILE 92 B VAL 93 n 93 VAL 93 B ASN 94 n 94 ASN 94 B ARG 95 n 95 ARG 95 B PHE 96 n 96 PHE 96 B VAL 97 n 97 VAL 97 B GLU 98 n 98 GLU 98 B THR 99 n 99 THR 99 B GLN 100 n 100 GLN 100 B THR 101 n 101 THR 101 B ASN 102 n 102 ASN 102 B TYR 103 n 103 TYR 103 B GLU 104 n 104 GLU 104 B LYS 105 n 105 LYS 105 B LEU 106 n 106 LEU 106 B LYS 107 n 107 LYS 107 B ASN 108 n 108 ASN 108 B ARG 109 n 109 ARG 109 B LEU 110 n 110 LEU 110 B VAL 111 n 111 VAL 111 B GLN 112 n 112 GLN 112 B ASN 113 n 113 ASN 113 B ALA 114 n 114 ALA 114 B ARG 115 n 115 ARG 115 B VAL 116 n 116 VAL 116 B ALA 117 n 117 ALA 117 B ALA 118 n 118 ALA 118 B ARG 119 n 119 ARG 119 B GLN 120 n 120 GLN 120 B LYS 121 n 121 LYS 121 B GLU 122 n 122 GLU 122 B TYR 123 n 123 TYR 123 B THR 124 n 124 THR 124 B GLU 125 n 125 GLU 125 B ILE 126 n 126 ILE 126 B PRO 127 n 127 PRO 127 B ASP 128 n 128 ASP 128 B ILE 129 n 129 ILE 129 B PHE 130 n 130 PHE 130 B LEU 131 n 131 LEU 131 B CYS 132 n 132 CYS 132 B PRO 133 n 133 PRO 133 B ILE 134 n 134 ILE 134 B SER 135 n 135 SER 135 B LYS 136 n 136 LYS 136 B THR 137 n 137 THR 137 B LEU 138 n 138 LEU 138 B ILE 139 n 139 ILE 139 B LYS 140 n 140 LYS 140 B THR 141 n 141 THR 141 B PRO 142 n 142 PRO 142 B VAL 143 n 143 VAL 143 B ILE 144 n 144 ILE 144 B THR 145 n 145 THR 145 B ALA 146 n 146 ALA 146 B GLN 147 n 147 GLN 147 B GLY 148 n 148 GLY 148 B LYS 149 n 149 LYS 149 B VAL 150 n 150 VAL 150 B TYR 151 n 151 TYR 151 B ASP 152 n 152 ASP 152 B GLN 153 n 153 GLN 153 B GLU 154 n 154 GLU 154 B ALA 155 n 155 ALA 155 B LEU 156 n 156 LEU 156 B SER 157 n 157 SER 157 B ASN 158 n 158 ASN 158 B PHE 159 n 159 PHE 159 B LEU 160 n 160 LEU 160 B ILE 161 n 161 ILE 161 B ALA 162 n 162 ALA 162 B THR 163 n 163 THR 163 B GLY 164 n 164 GLY 164 B ASN 165 n 165 ASN 165 B LYS 166 n 166 LYS 166 B ASP 167 n 167 ASP 167 B GLU 168 n 168 GLU 168 B THR 169 n 169 THR 169 B GLY 170 n 170 GLY 170 B LYS 171 n 171 LYS 171 B LYS 172 n 172 LYS 172 B LEU 173 n 173 LEU 173 B SER 174 n 174 SER 174 B ILE 175 n 175 ILE 175 B ASP 176 n 176 ASP 176 B ASP 177 n 177 ASP 177 B VAL 178 n 178 VAL 178 B VAL 179 n 179 VAL 179 B VAL 180 n 180 VAL 180 B PHE 181 n 181 PHE 181 B ASP 182 n 182 ASP 182 B GLU 183 n 183 GLU 183 B LEU 184 n 184 LEU 184 B TYR 185 n 185 TYR 185 B GLN 186 n 186 GLN 186 B n 187 187 B n 188 188 B n 189 189 B n 190 190 B n 191 191 B n 192 192 B n 193 193 B n 194 194 B n 195 195 B n 196 196 B n 197 197 B n 198 198 B n 199 199 B n 200 200 B n 201 201 B n 202 202 B n 203 203 B n 204 204 B n 205 205 B n 206 206 B n 207 207 B n 208 208 B n 209 209 B n 210 210 B n 211 211 B n 212 212 B n 213 213 B n 214 214 B n 215 215 B 3.1130 1.6507 2.4143 3.2676 -0.4040 3.0972 0.2494 -1.0676 -0.3933 0.4166 -0.1271 -0.8479 -0.5462 -0.1519 -0.0797 0.3713 0.0216 0.0903 0.4776 0.1134 0.5333 refined -36.0447 13.4072 10.1917 X-RAY DIFFRACTION 8.7445 6.0095 -5.4911 8.3195 -6.6932 8.2605 -0.1546 -1.3015 -0.7860 -0.4905 -0.2480 -1.2897 0.6995 1.4969 0.2197 0.2786 -0.0109 -0.1012 0.3968 0.0600 0.4997 refined -42.6781 4.1993 11.3687 X-RAY DIFFRACTION 5.7845 2.5585 -0.8116 4.6928 -2.4642 2.1108 0.0647 -0.0643 0.0572 0.1190 -0.0305 0.0750 -0.2893 -0.3685 -0.0364 0.2162 0.0425 -0.0127 0.2492 -0.0286 0.1197 refined -53.8599 9.5298 8.8761 X-RAY DIFFRACTION 6.4539 -3.2774 0.5669 7.7887 -1.5971 2.8351 -0.0514 -0.8599 -0.7663 0.7147 0.2822 1.1747 -0.4717 -0.3510 -0.1957 0.2474 -0.0330 0.0403 0.4609 0.0745 0.3259 refined -68.5512 3.1306 15.2142 X-RAY DIFFRACTION 3.1044 0.8909 1.5405 3.1385 0.5635 4.3426 -0.1789 0.1493 0.3520 -0.3036 0.1131 0.1467 0.0174 -0.2409 0.0141 0.2390 -0.0391 0.0762 0.2234 0.1187 0.2851 refined -37.1305 31.9078 5.1980 X-RAY DIFFRACTION 5.6280 -4.1611 6.6930 6.9491 -7.3053 9.2877 -0.0354 -0.1728 0.1510 -0.1741 -0.2681 -0.2508 0.1977 0.0273 0.2123 0.2446 0.0293 0.0914 0.2764 0.0446 0.2757 refined -11.1653 16.0065 20.9715 X-RAY DIFFRACTION 7.6716 -4.1121 -1.1678 3.1542 0.9486 1.1748 0.0454 -0.7006 -0.3260 1.1661 0.2846 0.7242 -0.8705 -0.2821 -0.2099 0.7866 0.0500 0.3506 0.4795 0.0889 0.5992 refined -19.9392 14.7119 33.3483 X-RAY DIFFRACTION X-RAY DIFFRACTION 1 chain A and resi 0:18 X-RAY DIFFRACTION 2 chain A and resi 19:38 X-RAY DIFFRACTION 3 chain A and resi 39:116 X-RAY DIFFRACTION 4 chain A and resi 117:147 X-RAY DIFFRACTION 5 chain B and resi 4:94 X-RAY DIFFRACTION 6 chain B and resi 95:122 X-RAY DIFFRACTION 7 chain B and resi 123:186 author_defined_assembly 2 dimeric B MSE 34 modified residue B MSE 34 MET 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 A N SER 22 A N SER 23 A O THR 36 A O THR 37 A N ILE 37 A N ILE 38 A O PHE 50 A O PHE 51 A N HIS 55 A N HIS 56 A O LYS 66 A O LYS 67 B O TYR 56 B O TYR 56 B N VAL 48 B N VAL 48 B N ILE 49 B N ILE 49 B O GLN 84 B O GLN 84 B O TYR 151 B O TYR 151 B N VAL 143 B N VAL 143 B N ILE 144 B N ILE 144 B O VAL 179 B O VAL 179 B N ASP 167 B N ASP 167 B O LYS 171 B O LYS 171 1 B MSE 1 B MSE 1 1 Y 1 B ALA 2 B ALA 2 1 Y 1 B THR 3 B THR 3 1 Y 1 B GLN 187 B GLN 187 1 Y 1 B ILE 188 B ILE 188 1 Y 1 B LYS 189 B LYS 189 1 Y 1 B VAL 190 B VAL 190 1 Y 1 B TYR 191 B TYR 191 1 Y 1 B ASN 192 B ASN 192 1 Y 1 B PHE 193 B PHE 193 1 Y 1 B TYR 194 B TYR 194 1 Y 1 B ARG 195 B ARG 195 1 Y 1 B LYS 196 B LYS 196 1 Y 1 B ARG 197 B ARG 197 1 Y 1 B GLU 198 B GLU 198 1 Y 1 B VAL 199 B VAL 199 1 Y 1 B GLN 200 B GLN 200 1 Y 1 B LYS 201 B LYS 201 1 Y 1 B ASN 202 B ASN 202 1 Y 1 B GLN 203 B GLN 203 1 Y 1 B ILE 204 B ILE 204 1 Y 1 B GLN 205 B GLN 205 1 Y 1 B PRO 206 B PRO 206 1 Y 1 B SER 207 B SER 207 1 Y 1 B VAL 208 B VAL 208 1 Y 1 B SER 209 B SER 209 1 Y 1 B ASN 210 B ASN 210 1 Y 1 B GLY 211 B GLY 211 1 Y 1 B PHE 212 B PHE 212 1 Y 1 B GLY 213 B GLY 213 1 Y 1 B PHE 214 B PHE 214 1 Y 1 B PHE 215 B PHE 215 1 Y 1 A ASP 16 -117.47 73.78 1 A GLN 20 -98.39 33.80 1 A SER 22 -169.67 117.19 1 A ALA 23 -121.15 -166.22 1 A ASP 28 -43.70 108.45 1 A ARG 90 -128.78 -117.68 1 A ASP 130 -161.45 77.44 1 B SER 41 66.15 -2.87 1 B LYS 69 -98.19 48.74 0.2228 0.1668 0.1697 2.70 35.855 968 10884 5.12 86.68 0.29 Random selection 1 FREE R-VALUE 1.36 MOLECULAR REPLACEMENT 22.03 0.90 1.11 4DDI, LubX U-box 1 WT PDB code 4WZ0 ML FLAT BULK SOLVENT MODEL 2.70 35.855 53 2706 0 0 2653 0.005 2746 0.903 3737 13.874 1055 0.044 417 0.007 484 0.3660 0.2443 2.8404 87 1563 53.00 0.2851 0.2306 3.0183 128 2170 74.00 0.2829 0.2112 3.2512 158 2699 91.00 0.2300 0.1831 3.5781 159 2912 98.00 0.1959 0.1467 4.0952 152 2895 98.00 0.1964 0.1283 5.1570 141 2890 97.00 0.1782 0.1569 35.8584 143 2805 95.00 2.70 40.00 4WZ3 11243 0.054 1 20.05 5.0 99.0 0.665 2.70 2.75 4.07 1 5.0 99.8 data reduction HKL-3000 phasing PHENIX model building PHENIX model building Coot refinement PHENIX (phenix.refine: 1.9_1692) data scaling HKL-3000 Crystal structure of the complex between LubX/LegU2/Lpp2887 U-box 1 and Homo sapiens UBE2D2 1 N N 2 N N 3 N N 3 N N A MET 1 A MET 2 HELX_P A LEU 13 A LEU 14 1 AA1 13 A LEU 86 A LEU 87 HELX_P A ARG 90 A ARG 91 5 AA2 5 A THR 98 A THR 99 HELX_P A ASP 112 A ASP 113 1 AA3 15 A VAL 120 A VAL 121 HELX_P A ASP 130 A ASP 131 1 AA4 11 A ASP 130 A ASP 131 HELX_P A ALA 146 A ALA 147 1 AA5 17 B ASP 10 B ASP 10 HELX_P B SER 26 B SER 26 1 AA6 17 B PRO 32 B PRO 32 HELX_P B THR 36 B THR 36 5 AA7 5 B LYS 58 B LYS 58 HELX_P B GLU 66 B GLU 66 1 AA8 9 B THR 79 B THR 79 HELX_P B LEU 83 B LEU 83 5 AA9 5 B LEU 89 B LEU 89 HELX_P B ARG 119 B ARG 119 1 AB1 31 B PRO 127 B PRO 127 HELX_P B LEU 131 B LEU 131 5 AB2 5 B GLN 153 B GLN 153 HELX_P B THR 163 B THR 163 1 AB3 11 B ASP 182 B ASP 182 HELX_P B TYR 185 B TYR 185 5 AB4 4 covale 1.325 both B THR 33 B C THR 33 1_555 B MSE 34 B N MSE 34 1_555 covale 1.331 both B MSE 34 B C MSE 34 1_555 B LEU 35 B N LEU 35 1_555 LIGASE alpha/beta protein, effector, activating enzyme, structural genomics, PSI-Biology, Midwest Center for Structural Genomics, MCSG, LIGASE A GLY 0 A GLY 1 1 A MET 1 A MET 2 -2.15 A ASP 28 A ASP 29 1 A ASP 29 A ASP 30 21.02 A TYR 60 A TYR 61 1 A PRO 61 A PRO 62 4.08 B GLU 168 B GLU 168 1 B THR 169 B THR 169 13.49 UB2D2_HUMAN UNP 1 1 P62837 MALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINS NGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM LUBX_LEGPA UNP 2 1 Q5X159 MATRNPFDIDHKSKYLREAALEANLSHPETTPTMLTCPIDSGFLKDPVITPEGFVYNKSSILKWLETKKEDPQSRKPLTA KDLQPFPELLIIVNRFVETQTNYEKLKNRLVQNARVAARQKEYTEIPDIFLCPISKTLIKTPVITAQGKVYDQEALSNFL IATGNKDETGKKLSIDDVVVFDELYQQIKVYNFYRKREVQKNQIQPSVSNGFGFF 1 147 4WZ3 1 147 P62837 A 1 2 148 1 215 4WZ3 1 215 Q5X159 B 2 1 215 1 expression tag GLY 0 4WZ3 A P62837 UNP 1 1 CYS engineered mutation SER 85 4WZ3 A P62837 UNP 85 86 4 3 3 2 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A CYS 21 A CYS 22 A SER 22 A SER 23 A HIS 32 A HIS 33 A MET 38 A MET 39 A VAL 49 A VAL 50 A HIS 55 A HIS 56 A LYS 66 A LYS 67 A PHE 69 A PHE 70 B VAL 55 B VAL 55 B ASN 57 B ASN 57 B PRO 47 B PRO 47 B ILE 49 B ILE 49 B GLN 84 B GLN 84 B PRO 85 B PRO 85 B VAL 150 B VAL 150 B ASP 152 B ASP 152 B PRO 142 B PRO 142 B ILE 144 B ILE 144 B VAL 179 B VAL 179 B VAL 180 B VAL 180 B LYS 166 B LYS 166 B ASP 167 B ASP 167 B LYS 171 B LYS 171 B LYS 172 B LYS 172 169 P 61