0.015002 0.008661 0.000000 0.000000 0.017323 0.000000 0.000000 0.000000 0.012163 0.00000 0.00000 0.00000 Yin, J. Bosanac, I. Ma, X. Hymowitz, S. Starovasnik, M. Cochran, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 66.658 66.658 82.218 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 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 US Nat.Struct.Mol.Biol. 1545-9993 19 171 175 10.1038/nsmb.2206 22245969 Phosphorylation-dependent activity of the deubiquitinase DUBA. 2012 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 CCD 2008-10-07 ADSC QUANTUM 315 a high resolution Si(311) cut and a lower resolution Si(111) MAD M x-ray 1 0.9798 1.0 ID29 ESRF 0.9798 SYNCHROTRON ESRF BEAMLINE ID29 21598.607 OTU domain-containing protein 5 3.4.19.12 catalytic or OTU domain (Residues 172-351) 3.4.19.12 1 man polymer 18.015 water 56 nat water Deubiquitinating enzyme A, DUBA no yes GSH(MSE)GAGYNSEDEYEAAAARIEA(MSE)DPATVEQQEHWFEKALRDKKGFIIKQ(MSE)KEDGACLFRAVADQVYG DQD(MSE)HEVVRKHC(MSE)DYL(MSE)KNADYFSNYVTEDFTTYINRKRKNNCHGNHIE(MSE)QA(MSE)AE(MSE) YNRPVEVYQYSTGTSAVEPINTFHGIHQNEDEPIRVSYHRNIHYNSVVNPNKATIGVGLG GSHMGAGYNSEDEYEAAAARIEAMDPATVEQQEHWFEKALRDKKGFIIKQMKEDGACLFRAVADQVYGDQDMHEVVRKHC MDYLMKNADYFSNYVTEDFTTYINRKRKNNCHGNHIEMQAMAEMYNRPVEVYQYSTGTSAVEPINTFHGIHQNEDEPIRV SYHRNIHYNSVVNPNKATIGVGLG A 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 human sample DUBA, OTUD5 9606 Homo sapiens 469008 Escherichia coli BL21-CodonPlus (DE3)-RIL PLASMID pET28B 1 2.44 49.62 THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS VAPOR DIFFUSION, SITTING DROP 7.0 0.8 M succinic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K 293 repository Initial release Database references 1 0 2012-01-11 1 1 2012-02-29 RCSB Y RCSB 2011-08-31 REL REL HOH water HOH 1 2 HOH HOH 1 A HOH 2 2 HOH HOH 2 A HOH 3 2 HOH HOH 3 A HOH 4 2 HOH HOH 4 A HOH 5 2 HOH HOH 5 A HOH 6 2 HOH HOH 6 A HOH 7 2 HOH HOH 7 A HOH 8 2 HOH HOH 8 A HOH 9 2 HOH HOH 9 A HOH 10 2 HOH HOH 10 A HOH 11 2 HOH HOH 11 A HOH 12 2 HOH HOH 12 A HOH 13 2 HOH HOH 13 A HOH 14 2 HOH HOH 14 A HOH 15 2 HOH HOH 15 A HOH 16 2 HOH HOH 16 A HOH 17 2 HOH HOH 17 A HOH 18 2 HOH HOH 18 A HOH 19 2 HOH HOH 19 A HOH 20 2 HOH HOH 20 A HOH 21 2 HOH HOH 21 A HOH 22 2 HOH HOH 22 A HOH 23 2 HOH HOH 23 A HOH 24 2 HOH HOH 24 A HOH 25 2 HOH HOH 25 A HOH 26 2 HOH HOH 26 A HOH 27 2 HOH HOH 27 A HOH 28 2 HOH HOH 28 A HOH 29 2 HOH HOH 29 A HOH 30 2 HOH HOH 30 A HOH 31 2 HOH HOH 31 A HOH 32 2 HOH HOH 32 A HOH 33 2 HOH HOH 33 A HOH 34 2 HOH HOH 34 A HOH 35 2 HOH HOH 35 A HOH 36 2 HOH HOH 36 A HOH 37 2 HOH HOH 37 A HOH 38 2 HOH HOH 38 A HOH 39 2 HOH HOH 39 A HOH 40 2 HOH HOH 40 A HOH 41 2 HOH HOH 41 A HOH 42 2 HOH HOH 42 A HOH 43 2 HOH HOH 43 A HOH 44 2 HOH HOH 44 A HOH 45 2 HOH HOH 45 A HOH 46 2 HOH HOH 46 A HOH 47 2 HOH HOH 47 A HOH 48 2 HOH HOH 48 A HOH 49 2 HOH HOH 49 A HOH 50 2 HOH HOH 50 A HOH 51 2 HOH HOH 51 A HOH 52 2 HOH HOH 52 A HOH 53 2 HOH HOH 53 A HOH 54 2 HOH HOH 54 A HOH 57 2 HOH HOH 57 A HOH 58 2 HOH HOH 58 A n 1 168 A n 2 169 A n 3 170 A n 4 171 A n 5 172 A n 6 173 A n 7 174 A n 8 175 A n 9 176 A n 10 177 A n 11 178 A n 12 179 A n 13 180 A n 14 181 A n 15 182 A n 16 183 A n 17 184 A ALA 185 n 18 ALA 185 A ALA 186 n 19 ALA 186 A ARG 187 n 20 ARG 187 A ILE 188 n 21 ILE 188 A GLU 189 n 22 GLU 189 A ALA 190 n 23 ALA 190 A MSE 191 n 24 MSE 191 A ASP 192 n 25 ASP 192 A PRO 193 n 26 PRO 193 A ALA 194 n 27 ALA 194 A THR 195 n 28 THR 195 A VAL 196 n 29 VAL 196 A GLU 197 n 30 GLU 197 A GLN 198 n 31 GLN 198 A GLN 199 n 32 GLN 199 A GLU 200 n 33 GLU 200 A HIS 201 n 34 HIS 201 A TRP 202 n 35 TRP 202 A PHE 203 n 36 PHE 203 A GLU 204 n 37 GLU 204 A LYS 205 n 38 LYS 205 A ALA 206 n 39 ALA 206 A LEU 207 n 40 LEU 207 A ARG 208 n 41 ARG 208 A ASP 209 n 42 ASP 209 A LYS 210 n 43 LYS 210 A LYS 211 n 44 LYS 211 A GLY 212 n 45 GLY 212 A PHE 213 n 46 PHE 213 A ILE 214 n 47 ILE 214 A ILE 215 n 48 ILE 215 A LYS 216 n 49 LYS 216 A GLN 217 n 50 GLN 217 A MSE 218 n 51 MSE 218 A LYS 219 n 52 LYS 219 A GLU 220 n 53 GLU 220 A ASP 221 n 54 ASP 221 A GLY 222 n 55 GLY 222 A ALA 223 n 56 ALA 223 A CYS 224 n 57 CYS 224 A LEU 225 n 58 LEU 225 A PHE 226 n 59 PHE 226 A ARG 227 n 60 ARG 227 A ALA 228 n 61 ALA 228 A VAL 229 n 62 VAL 229 A ALA 230 n 63 ALA 230 A ASP 231 n 64 ASP 231 A GLN 232 n 65 GLN 232 A VAL 233 n 66 VAL 233 A TYR 234 n 67 TYR 234 A GLY 235 n 68 GLY 235 A ASP 236 n 69 ASP 236 A GLN 237 n 70 GLN 237 A ASP 238 n 71 ASP 238 A MSE 239 n 72 MSE 239 A HIS 240 n 73 HIS 240 A GLU 241 n 74 GLU 241 A VAL 242 n 75 VAL 242 A VAL 243 n 76 VAL 243 A ARG 244 n 77 ARG 244 A LYS 245 n 78 LYS 245 A HIS 246 n 79 HIS 246 A CYS 247 n 80 CYS 247 A MSE 248 n 81 MSE 248 A ASP 249 n 82 ASP 249 A TYR 250 n 83 TYR 250 A LEU 251 n 84 LEU 251 A MSE 252 n 85 MSE 252 A LYS 253 n 86 LYS 253 A ASN 254 n 87 ASN 254 A ALA 255 n 88 ALA 255 A ASP 256 n 89 ASP 256 A TYR 257 n 90 TYR 257 A PHE 258 n 91 PHE 258 A SER 259 n 92 SER 259 A ASN 260 n 93 ASN 260 A TYR 261 n 94 TYR 261 A n 95 262 A n 96 263 A n 97 264 A n 98 265 A n 99 266 A n 100 267 A n 101 268 A n 102 269 A n 103 270 A n 104 271 A n 105 272 A n 106 273 A n 107 274 A n 108 275 A n 109 276 A n 110 277 A n 111 278 A HIS 279 n 112 HIS 279 A GLY 280 n 113 GLY 280 A ASN 281 n 114 ASN 281 A HIS 282 n 115 HIS 282 A ILE 283 n 116 ILE 283 A GLU 284 n 117 GLU 284 A MSE 285 n 118 MSE 285 A GLN 286 n 119 GLN 286 A ALA 287 n 120 ALA 287 A MSE 288 n 121 MSE 288 A ALA 289 n 122 ALA 289 A GLU 290 n 123 GLU 290 A MSE 291 n 124 MSE 291 A TYR 292 n 125 TYR 292 A ASN 293 n 126 ASN 293 A ARG 294 n 127 ARG 294 A PRO 295 n 128 PRO 295 A VAL 296 n 129 VAL 296 A GLU 297 n 130 GLU 297 A VAL 298 n 131 VAL 298 A TYR 299 n 132 TYR 299 A GLN 300 n 133 GLN 300 A TYR 301 n 134 TYR 301 A SER 302 n 135 SER 302 A THR 303 n 136 THR 303 A GLY 304 n 137 GLY 304 A THR 305 n 138 THR 305 A SER 306 n 139 SER 306 A ALA 307 n 140 ALA 307 A VAL 308 n 141 VAL 308 A GLU 309 n 142 GLU 309 A PRO 310 n 143 PRO 310 A ILE 311 n 144 ILE 311 A ASN 312 n 145 ASN 312 A THR 313 n 146 THR 313 A PHE 314 n 147 PHE 314 A HIS 315 n 148 HIS 315 A GLY 316 n 149 GLY 316 A ILE 317 n 150 ILE 317 A HIS 318 n 151 HIS 318 A GLN 319 n 152 GLN 319 A ASN 320 n 153 ASN 320 A GLU 321 n 154 GLU 321 A ASP 322 n 155 ASP 322 A GLU 323 n 156 GLU 323 A PRO 324 n 157 PRO 324 A ILE 325 n 158 ILE 325 A ARG 326 n 159 ARG 326 A VAL 327 n 160 VAL 327 A SER 328 n 161 SER 328 A TYR 329 n 162 TYR 329 A HIS 330 n 163 HIS 330 A ARG 331 n 164 ARG 331 A ASN 332 n 165 ASN 332 A ILE 333 n 166 ILE 333 A HIS 334 n 167 HIS 334 A TYR 335 n 168 TYR 335 A ASN 336 n 169 ASN 336 A SER 337 n 170 SER 337 A VAL 338 n 171 VAL 338 A VAL 339 n 172 VAL 339 A ASN 340 n 173 ASN 340 A PRO 341 n 174 PRO 341 A ASN 342 n 175 ASN 342 A n 176 343 A n 177 344 A n 178 345 A n 179 346 A n 180 347 A n 181 348 A n 182 349 A n 183 350 A n 184 351 A author_defined_assembly 1 monomeric software_defined_assembly PISA 2 dimeric 5250 -21 15150 A MSE 191 SELENOMETHIONINE A MSE 24 MET A MSE 218 SELENOMETHIONINE A MSE 51 MET A MSE 239 SELENOMETHIONINE A MSE 72 MET A MSE 248 SELENOMETHIONINE A MSE 81 MET A MSE 252 SELENOMETHIONINE A MSE 85 MET A MSE 285 SELENOMETHIONINE A MSE 118 MET A MSE 288 SELENOMETHIONINE A MSE 121 MET A MSE 291 SELENOMETHIONINE A MSE 124 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 4_665 -x+1,-y+1,z crystal symmetry operation 33.3290000000 57.7275213655 0.0000000000 A O PHE 314 A O PHE 147 A N VAL 296 A N VAL 129 A N GLU 297 A N GLU 130 A O ILE 325 A O ILE 158 1 A GLY 168 A GLY 1 1 Y 1 A SER 169 A SER 2 1 Y 1 A HIS 170 A HIS 3 1 Y 1 A MSE 171 A MSE 4 1 Y 1 A GLY 172 A GLY 5 1 Y 1 A ALA 173 A ALA 6 1 Y 1 A GLY 174 A GLY 7 1 Y 1 A TYR 175 A TYR 8 1 Y 1 A ASN 176 A ASN 9 1 Y 1 A SER 177 A SER 10 1 Y 1 A GLU 178 A GLU 11 1 Y 1 A ASP 179 A ASP 12 1 Y 1 A GLU 180 A GLU 13 1 Y 1 A TYR 181 A TYR 14 1 Y 1 A GLU 182 A GLU 15 1 Y 1 A ALA 183 A ALA 16 1 Y 1 A ALA 184 A ALA 17 1 Y 1 A VAL 262 A VAL 95 1 Y 1 A THR 263 A THR 96 1 Y 1 A GLU 264 A GLU 97 1 Y 1 A ASP 265 A ASP 98 1 Y 1 A PHE 266 A PHE 99 1 Y 1 A THR 267 A THR 100 1 Y 1 A THR 268 A THR 101 1 Y 1 A TYR 269 A TYR 102 1 Y 1 A ILE 270 A ILE 103 1 Y 1 A ASN 271 A ASN 104 1 Y 1 A ARG 272 A ARG 105 1 Y 1 A LYS 273 A LYS 106 1 Y 1 A ARG 274 A ARG 107 1 Y 1 A LYS 275 A LYS 108 1 Y 1 A ASN 276 A ASN 109 1 Y 1 A ASN 277 A ASN 110 1 Y 1 A CYS 278 A CYS 111 1 Y 1 A LYS 343 A LYS 176 1 Y 1 A ALA 344 A ALA 177 1 Y 1 A THR 345 A THR 178 1 Y 1 A ILE 346 A ILE 179 1 Y 1 A GLY 347 A GLY 180 1 Y 1 A VAL 348 A VAL 181 1 Y 1 A GLY 349 A GLY 182 1 Y 1 A LEU 350 A LEU 183 1 Y 1 A GLY 351 A GLY 184 1 Y 1 A A SG O CYS HOH 224 58 1.88 1 A A O O TYR HOH 261 32 1.94 1 A A O O HOH HOH 24 42 2.10 1 A SER 306 40.89 81.26 43.351 0.37 0.18 -0.00 0.37 -0.00 -0.55 0.925 0.915 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.27615 0.24308 0.24459 2.20 28.86 503 10073 4.8 99.73 6.184 0.163 RANDOM 1 THROUGHOUT SAD 0.214 0.80 0.80 1.40 MAXIMUM LIKELIHOOD MASK 2.20 28.86 56 1213 0 0 1157 0.010 0.021 1185 1.011 1.909 1599 5.165 5.000 139 33.357 24.571 70 15.434 15.000 200 10.701 15.000 7 0.079 0.200 161 0.004 0.021 938 0.797 1.500 702 1.539 2.000 1130 2.105 3.000 483 3.472 4.500 469 0.387 0.287 2.257 39 756 20 99.87 44.7 2.15 50.00 3TMO 22276 21875 0.062 1 19.9 4.5 98.2 2.15 2.23 3.0 1866 0.425 1 4.5 83.8 data collection HKL-2000 model building PHENIX refinement REFMAC 5.5.0109 data reduction HKL-2000 data scaling HKL-2000 phasing PHENIX OTU domain-containing protein 5 (E.C.3.4.19.12) The catalytic domain of human deubiquitinase DUBA 1 N N 2 N N A ALA 185 A ALA 18 HELX_P A ASP 192 A ASP 25 1 1 8 A ASP 192 A ASP 25 HELX_P A GLY 212 A GLY 45 1 2 21 A LEU 225 A LEU 58 HELX_P A GLY 235 A GLY 68 1 3 11 A ASP 236 A ASP 69 HELX_P A ASP 238 A ASP 71 5 4 3 A MSE 239 A MSE 72 HELX_P A ASN 254 A ASN 87 1 5 16 A ASN 254 A ASN 87 HELX_P A SER 259 A SER 92 1 6 6 A GLY 280 A GLY 113 HELX_P A TYR 292 A TYR 125 1 7 13 covale 1.337 A ALA 190 A C ALA 23 1_555 A MSE 191 A N MSE 24 1_555 covale 1.333 A MSE 191 A C MSE 24 1_555 A ASP 192 A N ASP 25 1_555 covale 1.331 A GLN 217 A C GLN 50 1_555 A MSE 218 A N MSE 51 1_555 covale 1.328 A MSE 218 A C MSE 51 1_555 A LYS 219 A N LYS 52 1_555 covale 1.323 A ASP 238 A C ASP 71 1_555 A MSE 239 A N MSE 72 1_555 covale 1.331 A MSE 239 A C MSE 72 1_555 A HIS 240 A N HIS 73 1_555 covale 1.329 A CYS 247 A C CYS 80 1_555 A MSE 248 A N MSE 81 1_555 covale 1.329 A MSE 248 A C MSE 81 1_555 A ASP 249 A N ASP 82 1_555 covale 1.331 A LEU 251 A C LEU 84 1_555 A MSE 252 A N MSE 85 1_555 covale 1.330 A MSE 252 A C MSE 85 1_555 A LYS 253 A N LYS 86 1_555 covale 1.330 A GLU 284 A C GLU 117 1_555 A MSE 285 A N MSE 118 1_555 covale 1.327 A MSE 285 A C MSE 118 1_555 A GLN 286 A N GLN 119 1_555 covale 1.329 A ALA 287 A C ALA 120 1_555 A MSE 288 A N MSE 121 1_555 covale 1.325 A MSE 288 A C MSE 121 1_555 A ALA 289 A N ALA 122 1_555 covale 1.334 A GLU 290 A C GLU 123 1_555 A MSE 291 A N MSE 124 1_555 covale 1.329 A MSE 291 A C MSE 124 1_555 A TYR 292 A N TYR 125 1_555 HYDROLASE OTU fold, Deubiquitinase, phosphorylation, HYDROLASE OTUD5_HUMAN UNP 1 172 Q96G74 GAGYNSEDEYEAAAARIEAMDPATVEQQEHWFEKALRDKKGFIIKQMKEDGACLFRAVADQVYGDQDMHEVVRKHCMDYL MKNADYFSNYVTEDFTTYINRKRKNNCHGNHIEMQAMAEMYNRPVEVYQYSTGTSAVEPINTFHGIHQNEDEPIRVSYHR NIHYNSVVNPNKATIGVGLG 172 351 3TMO 172 351 Q96G74 A 1 5 184 1 EXPRESSION TAG GLY 168 3TMO A Q96G74 UNP 1 1 EXPRESSION TAG SER 169 3TMO A Q96G74 UNP 2 1 EXPRESSION TAG HIS 170 3TMO A Q96G74 UNP 3 1 EXPRESSION TAG MSE 171 3TMO A Q96G74 UNP 4 3 anti-parallel parallel A ASN 312 A ASN 145 A PHE 314 A PHE 147 A VAL 296 A VAL 129 A GLN 300 A GLN 133 A ILE 325 A ILE 158 A TYR 329 A TYR 162 172 P 64