0.018136 0.000000 0.000000 -0.000000 0.018136 0.000000 0.000000 -0.000000 0.009478 0.00000 0.00000 0.00000 Kristariyanto, Y.A. Abdul Rehman, S.A. Kulathu, Y. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 16 90.00 90.00 90.00 55.140 55.140 105.510 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 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 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 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 S C N 76 N C N 77 N O N 78 N C N 79 N C N 80 N C N 81 N O N 82 N N N 83 N O N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N N N 95 S C N 96 N C N 97 N O N 98 N C N 99 N C N 100 N C N 101 N O N 102 N O N 103 N O N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N N N 114 N C N 115 N C 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 N N 124 S C N 125 N C N 126 N O N 127 N C Y 128 N C Y 129 N N Y 130 N C Y 131 N C Y 132 N N N 133 N O N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N O N 145 N H N 146 N H N 147 N N N 148 S C N 149 N C N 150 N O N 151 S C N 152 N C N 153 N C N 154 N C N 155 N O N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H 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 N N 170 S C N 171 N C N 172 N O N 173 N C N 174 N C N 175 N C N 176 N C N 177 N O N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H 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 N N 192 S C N 193 N C N 194 N O N 195 N C N 196 N C N 197 N C N 198 N C N 199 N N N 200 N O N 201 N H N 202 N H N 203 N H N 204 N H N 205 N H 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 N N 217 S C N 218 N C N 219 N O N 220 N C N 221 N C N 222 N S N 223 N C N 224 N O N 225 N H N 226 N H N 227 N H N 228 N H 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 N N 237 S C N 238 N C N 239 N O N 240 N C Y 241 N C Y 242 N C Y 243 N C Y 244 N C Y 245 N C Y 246 N C N 247 N O N 248 N H N 249 N H N 250 N H N 251 N H N 252 N H 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 N N 260 S C N 261 N C N 262 N O N 263 N C N 264 N C N 265 N C N 266 N O N 267 N H N 268 N H N 269 N H N 270 N H N 271 N H N 272 N H N 273 N H N 274 N H N 275 N H N 276 N N N 277 S C N 278 N C N 279 N O N 280 N C N 281 N O N 282 N O 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 N N 291 S C N 292 N C N 293 N O N 294 R C N 295 N O N 296 N C N 297 N O 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 H N 305 N H N 306 N H N 307 N N N 308 S C N 309 N C N 310 N O N 311 N C Y 312 N C Y 313 N C Y 314 N C Y 315 N C Y 316 N C Y 317 N C N 318 N O N 319 N O N 320 N H N 321 N H N 322 N H N 323 N H N 324 N H N 325 N H N 326 N H N 327 N H N 328 N H N 329 N H N 330 N H N 331 N N N 332 S C N 333 N C N 334 N O N 335 N C N 336 N C N 337 N C N 338 N O N 339 N H N 340 N H N 341 N H N 342 N H N 343 N H N 344 N H N 345 N H N 346 N H N 347 N H N 348 N H N 349 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 doub N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N doub N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N doub N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N doub N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N doub N 123 N sing N 124 N sing N 125 N sing N 126 N sing Y 127 N sing Y 128 N doub Y 129 N doub N 130 N sing Y 131 N sing N 132 N sing Y 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 doub N 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 sing 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 doub 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 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 doub 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 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 doub 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 sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N doub N 231 N sing N 232 N sing N 233 N sing N 234 N sing Y 235 N doub Y 236 N sing Y 237 N sing N 238 N sing Y 239 N doub N 240 N sing Y 241 N doub N 242 N sing Y 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 doub 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 sing N 263 N sing N 264 N sing N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N doub 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 sing N 280 N sing N 281 N sing N 282 N sing N 283 N doub 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 sing N 297 N sing N 298 N sing N 299 N doub N 300 N sing N 301 N sing N 302 N sing N 303 N sing Y 304 N doub Y 305 N sing Y 306 N sing N 307 N sing Y 308 N doub N 309 N sing Y 310 N doub N 311 N sing Y 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 doub 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 sing N 332 N sing N 333 N sing N 334 N sing UK EMBO Rep. 1469-3178 18 392 402 10.15252/embr.201643205 28082312 A single MIU motif of MINDY-1 recognizes K48-linked polyubiquitin chains. 2017 10.2210/pdb5mn9/pdb pdb_00005mn9 100 1 PIXEL 2015-05-01 DECTRIS PILATUS3 2M single crystal SINGLE WAVELENGTH M x-ray 1 0.96769 1.0 MASSIF-1 ESRF 0.96769 SYNCHROTRON ESRF BEAMLINE MASSIF-1 8576.831 Ubiquitin-40S ribosomal protein S27a 2 nat polymer 4939.382 Ubiquitin carboxyl-terminal hydrolase MINDY-1 3.4.19.12 1 man polymer 18.015 water 3 nat water Ubiquitin carboxyl extension protein 80 Deubiquitinating enzyme MINDY-1,Protein FAM63A no no MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG A,B polypeptide(L) no no GPLGSQVDQDYLIALSLQQQQPRGPLGLTDLELAQQLQQEEYQQ GPLGSQVDQDYLIALSLQQQQPRGPLGLTDLELAQQLQQEEYQQ C 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 Human sample 1 44 FAM63A, KIAA1390 9606 Homo sapiens 469008 Escherichia coli BL21(DE3) Biological sequence Bovine sample 1 76 9913 Bos taurus 1 1.82 32.23 VAPOR DIFFUSION, HANGING DROP 5.4 100 mM sodium acetate pH 5.4 and 18.5 % PEG3350 293.15 diffrn_source pdbx_audit_support chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_ncs_dom_lim repository Initial release Database references Data collection Author supporting evidence Data collection Database references Refinement description 1 0 2017-01-25 1 1 2017-03-15 1 2 2017-07-05 1 3 2017-08-30 1 4 2024-01-17 _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.type _pdbx_audit_support.funding_organization _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ncs_dom_lim.beg_auth_comp_id _struct_ncs_dom_lim.beg_label_asym_id _struct_ncs_dom_lim.beg_label_comp_id _struct_ncs_dom_lim.beg_label_seq_id _struct_ncs_dom_lim.end_auth_comp_id _struct_ncs_dom_lim.end_label_asym_id _struct_ncs_dom_lim.end_label_comp_id _struct_ncs_dom_lim.end_label_seq_id United Kingdom Medical Research Council (United Kingdom) MC_UU_12016/6 N PDBE Y PDBE 2016-12-13 REL REL HOH water 1UBQ PDB experimental model HOH 2 3 HOH HOH 101 B HOH 3 3 HOH HOH 102 B HOH 1 3 HOH HOH 501 C MET 1 n 1 MET 1 A GLN 2 n 2 GLN 2 A ILE 3 n 3 ILE 3 A PHE 4 n 4 PHE 4 A VAL 5 n 5 VAL 5 A LYS 6 n 6 LYS 6 A THR 7 n 7 THR 7 A LEU 8 n 8 LEU 8 A THR 9 n 9 THR 9 A GLY 10 n 10 GLY 10 A LYS 11 n 11 LYS 11 A THR 12 n 12 THR 12 A ILE 13 n 13 ILE 13 A THR 14 n 14 THR 14 A LEU 15 n 15 LEU 15 A GLU 16 n 16 GLU 16 A VAL 17 n 17 VAL 17 A GLU 18 n 18 GLU 18 A PRO 19 n 19 PRO 19 A SER 20 n 20 SER 20 A ASP 21 n 21 ASP 21 A THR 22 n 22 THR 22 A ILE 23 n 23 ILE 23 A GLU 24 n 24 GLU 24 A ASN 25 n 25 ASN 25 A VAL 26 n 26 VAL 26 A LYS 27 n 27 LYS 27 A ALA 28 n 28 ALA 28 A LYS 29 n 29 LYS 29 A ILE 30 n 30 ILE 30 A GLN 31 n 31 GLN 31 A ASP 32 n 32 ASP 32 A LYS 33 n 33 LYS 33 A GLU 34 n 34 GLU 34 A GLY 35 n 35 GLY 35 A ILE 36 n 36 ILE 36 A PRO 37 n 37 PRO 37 A PRO 38 n 38 PRO 38 A ASP 39 n 39 ASP 39 A GLN 40 n 40 GLN 40 A GLN 41 n 41 GLN 41 A ARG 42 n 42 ARG 42 A LEU 43 n 43 LEU 43 A ILE 44 n 44 ILE 44 A PHE 45 n 45 PHE 45 A ALA 46 n 46 ALA 46 A GLY 47 n 47 GLY 47 A LYS 48 n 48 LYS 48 A GLN 49 n 49 GLN 49 A LEU 50 n 50 LEU 50 A GLU 51 n 51 GLU 51 A ASP 52 n 52 ASP 52 A GLY 53 n 53 GLY 53 A ARG 54 n 54 ARG 54 A THR 55 n 55 THR 55 A LEU 56 n 56 LEU 56 A SER 57 n 57 SER 57 A ASP 58 n 58 ASP 58 A TYR 59 n 59 TYR 59 A ASN 60 n 60 ASN 60 A ILE 61 n 61 ILE 61 A GLN 62 n 62 GLN 62 A LYS 63 n 63 LYS 63 A GLU 64 n 64 GLU 64 A SER 65 n 65 SER 65 A THR 66 n 66 THR 66 A LEU 67 n 67 LEU 67 A HIS 68 n 68 HIS 68 A LEU 69 n 69 LEU 69 A VAL 70 n 70 VAL 70 A LEU 71 n 71 LEU 71 A ARG 72 n 72 ARG 72 A LEU 73 n 73 LEU 73 A n 74 74 A n 75 75 A n 76 76 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 n 1 383 C n 2 384 C n 3 385 C n 4 386 C n 5 387 C n 6 388 C n 7 389 C n 8 390 C n 9 391 C n 10 392 C n 11 393 C n 12 394 C n 13 395 C n 14 396 C n 15 397 C n 16 398 C n 17 399 C n 18 400 C n 19 401 C n 20 402 C n 21 403 C n 22 404 C n 23 405 C n 24 406 C n 25 407 C LEU 408 n 26 LEU 408 C GLY 409 n 27 GLY 409 C LEU 410 n 28 LEU 410 C THR 411 n 29 THR 411 C ASP 412 n 30 ASP 412 C LEU 413 n 31 LEU 413 C GLU 414 n 32 GLU 414 C LEU 415 n 33 LEU 415 C ALA 416 n 34 ALA 416 C GLN 417 n 35 GLN 417 C GLN 418 n 36 GLN 418 C LEU 419 n 37 LEU 419 C GLN 420 n 38 GLN 420 C GLN 421 n 39 GLN 421 C GLU 422 n 40 GLU 422 C GLU 423 n 41 GLU 423 C TYR 424 n 42 TYR 424 C GLN 425 n 43 GLN 425 C GLN 426 n 44 GLN 426 C 4.3672 0.3910 0.3667 9.1965 0.7937 3.9392 -0.0981 -0.2760 0.0822 0.0898 0.1216 1.0675 0.1268 -0.3963 -0.0235 0.0106 -0.0017 -0.0054 0.1068 -0.0049 0.1731 refined 14.1410 91.3920 3.0630 X-RAY DIFFRACTION 6.6267 -0.1177 -1.5525 7.7721 -3.1544 6.0599 -0.2436 -0.0716 0.0742 0.0398 0.6059 1.1527 -0.0871 -0.6003 -0.3622 0.0184 0.0389 0.0235 0.1723 0.1804 0.2877 refined 13.6370 118.8300 10.0330 X-RAY DIFFRACTION 5.2680 -3.3551 2.1336 12.7384 -6.4958 7.0560 -0.1961 0.1189 0.1128 -0.0413 0.1210 -0.2621 -0.0023 0.1250 0.0751 0.0345 -0.0136 -0.0055 0.0910 -0.0618 0.0538 refined 24.6760 101.7680 5.9740 X-RAY DIFFRACTION A 1 A 73 X-RAY DIFFRACTION 1 B 1 B 76 X-RAY DIFFRACTION 2 C 408 C 426 X-RAY DIFFRACTION 3 author_and_software_defined_assembly PISA 3 trimeric 1870 -11 9280 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 O ILE 13 A O ILE 13 A N VAL 5 A N VAL 5 A N PHE 4 A N PHE 4 A O LEU 67 A O LEU 67 A O VAL 70 A O VAL 70 A N ARG 42 A N ARG 42 A N PHE 45 A N PHE 45 A O LYS 48 A O LYS 48 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 B CG GLU 18 B CG GLU 18 1 Y 1 B CD GLU 18 B CD GLU 18 1 Y 1 B OE1 GLU 18 B OE1 GLU 18 1 Y 1 B OE2 GLU 18 B OE2 GLU 18 1 Y 1 B CG GLU 24 B CG GLU 24 1 Y 1 B CD GLU 24 B CD GLU 24 1 Y 1 B OE1 GLU 24 B OE1 GLU 24 1 Y 1 B OE2 GLU 24 B OE2 GLU 24 1 Y 1 A ARG 74 A ARG 74 1 Y 1 A GLY 75 A GLY 75 1 Y 1 A GLY 76 A GLY 76 1 Y 1 C GLY 383 C GLY 1 1 Y 1 C PRO 384 C PRO 2 1 Y 1 C LEU 385 C LEU 3 1 Y 1 C GLY 386 C GLY 4 1 Y 1 C SER 387 C SER 5 1 Y 1 C GLN 388 C GLN 6 1 Y 1 C VAL 389 C VAL 7 1 Y 1 C ASP 390 C ASP 8 1 Y 1 C GLN 391 C GLN 9 1 Y 1 C ASP 392 C ASP 10 1 Y 1 C TYR 393 C TYR 11 1 Y 1 C LEU 394 C LEU 12 1 Y 1 C ILE 395 C ILE 13 1 Y 1 C ALA 396 C ALA 14 1 Y 1 C LEU 397 C LEU 15 1 Y 1 C SER 398 C SER 16 1 Y 1 C LEU 399 C LEU 17 1 Y 1 C GLN 400 C GLN 18 1 Y 1 C GLN 401 C GLN 19 1 Y 1 C GLN 402 C GLN 20 1 Y 1 C GLN 403 C GLN 21 1 Y 1 C PRO 404 C PRO 22 1 Y 1 C ARG 405 C ARG 23 1 Y 1 C GLY 406 C GLY 24 1 Y 1 C PRO 407 C PRO 25 1 Y 58.638 0.34 -0.00 -0.00 0.34 -0.00 -0.69 0.971 0.958 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.22341 0.18268 0.18484 2.05 48.87 517 9368 5.2 99.97 13.654 0.162 RANDOM 1 THROUGHOUT MOLECULAR REPLACEMENT 0.221 0.177 0.70 0.70 1.20 1UBQ 2.05 48.87 3 1335 0 0 1332 0.010 0.019 1352 0.002 0.020 1368 1.441 1.997 1819 0.904 3.000 3160 6.100 5.000 165 38.290 26.406 64 14.185 15.000 276 13.893 15.000 7 0.081 0.200 217 0.005 0.020 1496 0.001 0.020 271 3.035 3.426 669 3.014 3.425 668 3.804 5.120 831 3.808 5.123 832 3.950 3.919 681 3.947 3.925 682 6.165 5.709 989 7.303 39.656 1354 7.313 39.683 1355 1 A 1 4160 X-RAY DIFFRACTION interatomic distance 0.11 0.05 2 B 1 4160 X-RAY DIFFRACTION interatomic distance 0.11 0.05 0.303 0.255 2.103 39 674 20 100.00 2.05 48.87 5MN9 9899 0.999 0.043 1 19.4 6.6 100 0.544 2.05 2.11 2.9 0.818 1 6.6 100 data reduction XDS phasing PHASER refinement REFMAC 5.8.0155 data scaling XDS N Crystal structure of MINDY-1 tMIU in complex with K48-diUb 1 N N 1 N N 2 N N 3 N N 3 N N A THR 22 A THR 22 HELX_P A GLY 35 A GLY 35 1 AA1 14 A PRO 37 A PRO 37 HELX_P A ASP 39 A ASP 39 5 AA2 3 A LEU 56 A LEU 56 HELX_P A ASN 60 A ASN 60 5 AA3 5 B THR 22 B THR 22 HELX_P B GLY 35 B GLY 35 1 AA4 14 B PRO 37 B PRO 37 HELX_P B ASP 39 B ASP 39 5 AA5 3 B LEU 56 B LEU 56 HELX_P B ASN 60 B ASN 60 5 AA6 5 C LEU 410 C LEU 28 HELX_P C GLN 426 C GLN 44 1 AA7 17 HYDROLASE MOTIF INTERACTING WITH UBIQUITIN, UBIQUITIN BINDING DOMAIN, HYDROLASE AND CYSTEINE PROTEASE, HYDROLASE A B A MET 1 A MET 1 A ARG 72 A ARG 72 0 B MET 1 B MET 1 B ARG 72 B ARG 72 0 RS27A_BOVIN UNP 1 1 P62992 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG FA63A_HUMAN UNP 2 388 Q8N5J2 QVDQDYLIALSLQQQQPRGPLGLTDLELAQQLQQEEYQQ 1 76 5MN9 1 76 P62992 A 1 1 76 1 76 5MN9 1 76 P62992 B 1 1 76 388 426 5MN9 388 426 Q8N5J2 C 2 6 44 3 expression tag GLY 383 5MN9 C Q8N5J2 UNP 1 3 expression tag PRO 384 5MN9 C Q8N5J2 UNP 2 3 expression tag LEU 385 5MN9 C Q8N5J2 UNP 3 3 expression tag GLY 386 5MN9 C Q8N5J2 UNP 4 3 expression tag SER 387 5MN9 C Q8N5J2 UNP 5 5 5 anti-parallel parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel A THR 12 A THR 12 A GLU 16 A GLU 16 A GLN 2 A GLN 2 A THR 7 A THR 7 A THR 66 A THR 66 A LEU 71 A LEU 71 A GLN 41 A GLN 41 A PHE 45 A PHE 45 A LYS 48 A LYS 48 A GLN 49 A GLN 49 B THR 12 B THR 12 B GLU 16 B GLU 16 B GLN 2 B GLN 2 B THR 7 B THR 7 B THR 66 B THR 66 B LEU 71 B LEU 71 B GLN 41 B GLN 41 B PHE 45 B PHE 45 B LYS 48 B LYS 48 B GLN 49 B GLN 49 80 I 41