0.025719 0.014849 0.000000 0.000000 0.029698 0.000000 0.000000 0.000000 0.020001 0.00000 0.00000 0.00000 Qi, S. O'Hayre, M. Gutkind, J.S. Hurley, J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.000 90.000 120.000 38.882 38.882 49.997 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 C H5 N3 59.070 GUANIDINE non-polymer 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 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 C N 75 N N N 76 N N N 77 N N N 78 N H N 79 N H N 80 N H N 81 N H N 82 N H N 83 N N N 84 S C N 85 N C N 86 N O N 87 N C N 88 N C N 89 N C N 90 N O N 91 N O N 92 N O N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N N N 103 N C N 104 N C N 105 N O N 106 N O N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N N N 113 S C N 114 N C N 115 N O N 116 N C Y 117 N C Y 118 N N Y 119 N C Y 120 N C Y 121 N N N 122 N O N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N H N 133 N O N 134 N H N 135 N H N 136 N N N 137 S C N 138 N C N 139 N O N 140 S C N 141 N C N 142 N C N 143 N C N 144 N O 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 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 N N 159 S C N 160 N C N 161 N O N 162 N C N 163 N C N 164 N C N 165 N C N 166 N O N 167 N H N 168 N H N 169 N H 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 N N 181 S C N 182 N C N 183 N O N 184 N C N 185 N C N 186 N C N 187 N C N 188 N N N 189 N O 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 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 S N 212 N C N 213 N O N 214 N H 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 N N 226 S C N 227 N C N 228 N O N 229 N C Y 230 N C Y 231 N C Y 232 N C Y 233 N C Y 234 N C Y 235 N C N 236 N O 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 H N 245 N H N 246 N H N 247 N H N 248 N N N 249 S C N 250 N C N 251 N O N 252 N C N 253 N C N 254 N C N 255 N O 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 H N 265 N N N 266 S C N 267 N C N 268 N O N 269 N C N 270 N O N 271 N O N 272 N H N 273 N H N 274 N H N 275 N H N 276 N H N 277 N H N 278 N H N 279 N N N 280 S C N 281 N C N 282 N O N 283 R C N 284 N O N 285 N C N 286 N O 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 H N 294 N H N 295 N H N 296 N N N 297 S C N 298 N C N 299 N O N 300 N C Y 301 N C Y 302 N C Y 303 N C Y 304 N N Y 305 N C Y 306 N C Y 307 N C Y 308 N C Y 309 N C 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 H N 319 N H N 320 N H N 321 N H N 322 N H N 323 N N N 324 S C N 325 N C N 326 N O N 327 N C Y 328 N C Y 329 N C Y 330 N C Y 331 N C Y 332 N C Y 333 N C N 334 N O N 335 N O N 336 N H N 337 N H N 338 N H 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 N N 348 S C N 349 N C N 350 N O N 351 N C N 352 N C N 353 N C N 354 N O 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 H N 363 N H N 364 N H N 365 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 doub N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing 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 doub N 93 N sing N 94 N sing N 95 N sing 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 doub N 103 N sing 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 doub N 112 N sing N 113 N sing N 114 N sing N 115 N sing Y 116 N sing Y 117 N doub Y 118 N doub N 119 N sing Y 120 N sing N 121 N sing Y 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing 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 doub 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 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 doub 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 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 doub 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 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 doub N 220 N sing N 221 N sing N 222 N sing N 223 N sing Y 224 N doub Y 225 N sing Y 226 N sing N 227 N sing Y 228 N doub N 229 N sing Y 230 N doub N 231 N sing Y 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 doub 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 sing N 257 N sing N 258 N sing N 259 N doub 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 sing N 271 N sing N 272 N doub 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 sing N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N doub N 289 N sing N 290 N sing N 291 N sing N 292 N sing Y 293 N doub Y 294 N sing Y 295 N sing N 296 N sing Y 297 N doub Y 298 N sing Y 299 N sing N 300 N sing Y 301 N sing Y 302 N doub N 303 N sing Y 304 N doub N 305 N sing Y 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 sing N 316 N doub N 317 N sing N 318 N sing N 319 N sing N 320 N sing Y 321 N doub Y 322 N sing Y 323 N sing N 324 N sing Y 325 N doub N 326 N sing Y 327 N doub N 328 N sing Y 329 N sing N 330 N sing N 331 N sing N 332 N sing N 333 N sing N 334 N sing N 335 N sing N 336 N sing N 337 N sing N 338 N sing N 339 N sing N 340 N doub N 341 N sing N 342 N sing N 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 US J.Biol.Chem. JBCHA3 0071 0021-9258 289 4743 4752 10.1074/jbc.M113.527473 24379409 Structural and biochemical basis for ubiquitin ligase recruitment by arrestin-related domain-containing protein-3 (ARRDC3). 2014 10.2210/pdb4n7h/pdb pdb_00004n7h 100 1 IMAGE PLATE 2012-11-21 MAR scanner 300 mm plate SINGLE WAVELENGTH M x-ray 1 1.00000 1.0 22-ID APS 1.00000 SYNCHROTRON APS BEAMLINE 22-ID 4261.756 E3 ubiquitin-protein ligase NEDD4 3rd WW domain (UNP residues 840-872) 1 man polymer 1416.554 Arrestin domain-containing protein 3 1st PPXY Motif (UNP residues 342-354) 1 syn polymer 59.070 GUANIDINE 2 syn non-polymer 18.015 water 31 nat water Cell proliferation-inducing gene 53 protein, Neural precursor cell expressed developmentally down-regulated protein 4, NEDD-4 TBP-2-like inducible membrane protein, TLIMP no no AMGSGFLPKGWEVRHAPNGRPFFIDHNTKTTTWEDPR AMGSGFLPKGWEVRHAPNGRPFFIDHNTKTTTWEDPR A polypeptide(L) no no RPEAPPSYAEVVT RPEAPPSYAEVVT 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 human sample KIAA0093, NEDD4, NEDD4-1, PIG53 9606 Homo sapiens 469008 Escherichia coli Bl21(DE3) plasmid pGST-parallel2 1 1.94 36.64 VAPOR DIFFUSION, HANGING DROP 8.0 0.35M (NH4)SO4, 100mM Tris-HCl 8.0, 100mM Guanidine-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K 294 chem_comp_atom chem_comp_bond database_2 struct_ref_seq_dif struct_site repository Initial release Database references Database references Data collection Database references Derived calculations 1 0 2014-01-08 1 1 2014-02-05 1 2 2014-10-08 1 3 2024-02-28 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2013-10-15 REL REL GAI GUANIDINE HOH water 9606 human Homo sapiens sample GAI 1 3 GAI GAI 501 A GAI 2 3 GAI GAI 502 A HOH 2 4 HOH HOH 601 A HOH 3 4 HOH HOH 602 A HOH 4 4 HOH HOH 603 A HOH 6 4 HOH HOH 604 A HOH 8 4 HOH HOH 605 A HOH 9 4 HOH HOH 606 A HOH 10 4 HOH HOH 607 A HOH 11 4 HOH HOH 608 A HOH 12 4 HOH HOH 609 A HOH 13 4 HOH HOH 610 A HOH 16 4 HOH HOH 611 A HOH 17 4 HOH HOH 612 A HOH 19 4 HOH HOH 613 A HOH 20 4 HOH HOH 614 A HOH 23 4 HOH HOH 615 A HOH 24 4 HOH HOH 616 A HOH 27 4 HOH HOH 617 A HOH 31 4 HOH HOH 618 A HOH 34 4 HOH HOH 619 A HOH 44 4 HOH HOH 620 A HOH 45 4 HOH HOH 621 A HOH 5 4 HOH HOH 401 B HOH 7 4 HOH HOH 402 B HOH 14 4 HOH HOH 403 B HOH 15 4 HOH HOH 404 B HOH 22 4 HOH HOH 405 B HOH 26 4 HOH HOH 406 B HOH 28 4 HOH HOH 407 B HOH 35 4 HOH HOH 408 B HOH 36 4 HOH HOH 409 B HOH 46 4 HOH HOH 410 B n 1 417 A n 2 418 A n 3 419 A n 4 420 A GLY 421 n 5 GLY 421 A PHE 422 n 6 PHE 422 A LEU 423 n 7 LEU 423 A PRO 424 n 8 PRO 424 A LYS 425 n 9 LYS 425 A GLY 426 n 10 GLY 426 A TRP 427 n 11 TRP 427 A GLU 428 n 12 GLU 428 A VAL 429 n 13 VAL 429 A ARG 430 n 14 ARG 430 A HIS 431 n 15 HIS 431 A ALA 432 n 16 ALA 432 A PRO 433 n 17 PRO 433 A ASN 434 n 18 ASN 434 A GLY 435 n 19 GLY 435 A ARG 436 n 20 ARG 436 A PRO 437 n 21 PRO 437 A PHE 438 n 22 PHE 438 A PHE 439 n 23 PHE 439 A ILE 440 n 24 ILE 440 A ASP 441 n 25 ASP 441 A HIS 442 n 26 HIS 442 A ASN 443 n 27 ASN 443 A THR 444 n 28 THR 444 A LYS 445 n 29 LYS 445 A THR 446 n 30 THR 446 A THR 447 n 31 THR 447 A THR 448 n 32 THR 448 A TRP 449 n 33 TRP 449 A GLU 450 n 34 GLU 450 A ASP 451 n 35 ASP 451 A PRO 452 n 36 PRO 452 A ARG 453 n 37 ARG 453 A n 1 342 B n 2 343 B GLU 344 n 3 GLU 344 B ALA 345 n 4 ALA 345 B PRO 346 n 5 PRO 346 B PRO 347 n 6 PRO 347 B SER 348 n 7 SER 348 B TYR 349 n 8 TYR 349 B ALA 350 n 9 ALA 350 B GLU 351 n 10 GLU 351 B VAL 352 n 11 VAL 352 B n 12 353 B n 13 354 B author_and_software_defined_assembly PISA 2 dimeric 1010 -5 3280 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 GLU 428 A N GLU 12 A O ILE 440 A O ILE 24 A N PHE 439 A N PHE 23 A O THR 448 A O THR 32 1 A GAI 501 C GAI 1 A GAI 501 C GAI 1 A HOH 615 E HOH 1 A ALA 417 A ALA 1 1 Y 1 A MET 418 A MET 2 1 Y 1 A GLY 419 A GLY 3 1 Y 1 A SER 420 A SER 4 1 Y 1 B ARG 342 B ARG 1 1 Y 1 B PRO 343 B PRO 2 1 Y 1 B VAL 353 B VAL 12 1 Y 1 B THR 354 B THR 13 1 Y 71.130 29.4486 16.580 0.2331 0.1888 0.1907 1.6980 33.6730 235 4874 5109 4.6000 99.6100 1.000 0.510 0.7813 0.1900 1 1.370 26.0500 0.9000 1.1100 ML FLAT BULK SOLVENT MODEL 1.6980 33.6730 31 385 8 0 346 0.011 366 1.291 498 0.049 47 0.008 68 15.743 130 0.2663 0.1933 2.1396 112 2395 2507 2 100.0000 0.2249 0.1877 33.6794 123 2479 2602 2 99.0000 26.010 1.700 50.000 4N7H 5129 0.068 1.178 1 24.500 13.300 99.600 0.210 1.700 1.760 508 1.233 1 11.100 99.400 0.174 1.760 1.830 485 1.201 1 13.400 99.800 0.145 1.830 1.910 514 1.223 1 14.000 100.000 0.118 1.910 2.020 498 1.242 1 13.900 100.000 0.105 2.020 2.140 506 1.218 1 14.100 100.000 0.098 2.140 2.310 499 1.134 1 13.800 100.000 0.093 2.310 2.540 516 1.113 1 14.000 100.000 0.081 2.540 2.910 516 1.149 1 13.800 99.800 0.063 2.910 3.660 525 1.105 1 13.400 99.600 0.055 3.660 50.000 562 1.179 1 11.800 97.900 data reduction Zbyszek Otwinowski hkl@hkl-xray.com http://www.hkl-xray.com/ DENZO program data scaling Zbyszek Otwinowski hkl@hkl-xray.com http://www.hkl-xray.com/ SCALEPACK program refinement Paul D. Adams PDAdams@lbl.gov C++ http://www.phenix-online.org/ PHENIX package 1.8.3_1479 data extraction PDB deposit@deposit.rcsb.org April 22, 2011 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.11 data collection HKL-2000 data reduction HKL-2000 data scaling HKL-2000 Crystal Structure of the Complex of 3rd WW domain of Human Nedd4 and 1st PPXY Motif of ARRDC3 1 N N 2 N N 3 N N 3 N N 4 N N 4 N N B SER 348 B SER 7 HELX_P B VAL 352 B VAL 11 5 1 5 PROTEIN BINDING ww domain, Beta sheet, PPXY motif, PROTEIN BINDING NEDD4_HUMAN UNP 1 840 P46934 GFLPKGWEVRHAPNGRPFFIDHNTKTTTWEDPR ARRD3_HUMAN UNP 2 342 Q96B67 RPEAPPSYAEVVT 840 872 4N7H 421 453 P46934 A 1 5 37 342 354 4N7H 342 354 Q96B67 B 2 1 13 1 expression tag ALA 417 4N7H A P46934 UNP 1 1 expression tag MET 418 4N7H A P46934 UNP 2 1 expression tag GLY 419 4N7H A P46934 UNP 3 1 expression tag SER 420 4N7H A P46934 UNP 4 3 anti-parallel anti-parallel A TRP 427 A TRP 11 A HIS 431 A HIS 15 A PRO 437 A PRO 21 A ASP 441 A ASP 25 A THR 446 A THR 30 A THR 448 A THR 32 BINDING SITE FOR RESIDUE GAI A 501 A GAI 501 Software 9 BINDING SITE FOR RESIDUE GAI A 502 A GAI 502 Software 5 A TRP 427 A TRP 11 9 4_555 A TRP 427 A TRP 11 9 1_555 A ASP 441 A ASP 25 9 1_555 A ASP 441 A ASP 25 9 4_555 A THR 446 A THR 30 9 4_555 A THR 446 A THR 30 9 1_555 A THR 447 A THR 31 9 1_555 A THR 447 A THR 31 9 4_555 A THR 448 A THR 32 9 4_555 A ARG 430 A ARG 14 5 1_555 A HIS 431 A HIS 15 5 1_555 A ASP 451 A ASP 35 5 2_654 A HOH 602 E HOH 5 1_555 A HOH 613 E HOH 5 1_555 154 P 32 2 1