1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Tashiro, M. Okubo, S. Shimotakahara, S. Hatanaka, H. Yasuda, H. Kainosho, M. Yokoyama, S. Shindo, H. RIKEN Structural Genomics/Proteomics Initiative (RSGI) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 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 NE J.Biomol.NMR JBNME9 0800 0925-2738 25 153 156 10.1023/A:1022254432039 12652124 NMR structure of ubiquitin-like domain in PARKIN: Gene product of familial Parkinson's disease. 2003 UK Nature NATUAS 0006 0028-0836 392 605 608 10.1038/33416 Mutations in the parkin gene causes autosomal recessive juvenile parkinsonism 1998 10.2210/pdb1mg8/pdb pdb_00001mg8 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 8918.294 Parkin ubiquitin-like domain 1 nat polymer no no MGMIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRRR MGMIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRRR A trt001000160.1 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 house mouse Mus sample 10090 Mus musculus pET28b BL21 (DE3) RIKEN Structural Genomics/Proteomics Initiative RSGI database_2 pdbx_struct_assembly pdbx_struct_oper_list struct_ref_seq_dif struct_ref_seq_dif repository Initial release Version format compliance Version format compliance Database references Derived calculations Database references 1 0 2003-04-08 1 1 2008-04-28 1 2 2011-07-13 1 3 2022-02-23 1 4 2022-12-21 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ref_seq_dif.details _struct_ref_seq_dif.details Y RCSB Y PDBJ 2002-08-15 REL REL The structure was determined using triple-resonance NMR spectroscopy. structures with the lowest energy 50 10 3D_13C-separated_NOESY 3D_15N-separated_NOESY 5.0 ambient 298 K simulated annealing 1mM ubiquitin-like domain U-15N,13C; 25mM acetate buffer NA, 2mM dithiothreitol-d10 90% H2O/10% D2O refinement X-PLOR processing NMRPipe 500 Bruker DMX 600 Bruker DRX 600 Varian INOVA MET 1 n 1 MET 1 A GLY 2 n 2 GLY 2 A MET 3 n 3 MET 3 A ILE 4 n 4 ILE 4 A VAL 5 n 5 VAL 5 A PHE 6 n 6 PHE 6 A VAL 7 n 7 VAL 7 A ARG 8 n 8 ARG 8 A PHE 9 n 9 PHE 9 A ASN 10 n 10 ASN 10 A SER 11 n 11 SER 11 A SER 12 n 12 SER 12 A TYR 13 n 13 TYR 13 A GLY 14 n 14 GLY 14 A PHE 15 n 15 PHE 15 A PRO 16 n 16 PRO 16 A VAL 17 n 17 VAL 17 A GLU 18 n 18 GLU 18 A VAL 19 n 19 VAL 19 A ASP 20 n 20 ASP 20 A SER 21 n 21 SER 21 A ASP 22 n 22 ASP 22 A THR 23 n 23 THR 23 A SER 24 n 24 SER 24 A ILE 25 n 25 ILE 25 A LEU 26 n 26 LEU 26 A GLN 27 n 27 GLN 27 A LEU 28 n 28 LEU 28 A LYS 29 n 29 LYS 29 A GLU 30 n 30 GLU 30 A VAL 31 n 31 VAL 31 A VAL 32 n 32 VAL 32 A ALA 33 n 33 ALA 33 A LYS 34 n 34 LYS 34 A ARG 35 n 35 ARG 35 A GLN 36 n 36 GLN 36 A GLY 37 n 37 GLY 37 A VAL 38 n 38 VAL 38 A PRO 39 n 39 PRO 39 A ALA 40 n 40 ALA 40 A ASP 41 n 41 ASP 41 A GLN 42 n 42 GLN 42 A LEU 43 n 43 LEU 43 A ARG 44 n 44 ARG 44 A VAL 45 n 45 VAL 45 A ILE 46 n 46 ILE 46 A PHE 47 n 47 PHE 47 A ALA 48 n 48 ALA 48 A GLY 49 n 49 GLY 49 A LYS 50 n 50 LYS 50 A GLU 51 n 51 GLU 51 A LEU 52 n 52 LEU 52 A PRO 53 n 53 PRO 53 A ASN 54 n 54 ASN 54 A HIS 55 n 55 HIS 55 A LEU 56 n 56 LEU 56 A THR 57 n 57 THR 57 A VAL 58 n 58 VAL 58 A GLN 59 n 59 GLN 59 A ASN 60 n 60 ASN 60 A CYS 61 n 61 CYS 61 A ASP 62 n 62 ASP 62 A LEU 63 n 63 LEU 63 A GLU 64 n 64 GLU 64 A GLN 65 n 65 GLN 65 A GLN 66 n 66 GLN 66 A SER 67 n 67 SER 67 A ILE 68 n 68 ILE 68 A VAL 69 n 69 VAL 69 A HIS 70 n 70 HIS 70 A ILE 71 n 71 ILE 71 A VAL 72 n 72 VAL 72 A GLN 73 n 73 GLN 73 A ARG 74 n 74 ARG 74 A PRO 75 n 75 PRO 75 A ARG 76 n 76 ARG 76 A ARG 77 n 77 ARG 77 A ARG 78 n 78 ARG 78 A author_defined_assembly 1 monomeric 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 VAL 17 A O VAL 17 A N VAL 5 A N VAL 5 A N PHE 6 A N PHE 6 A O VAL 69 A O VAL 69 A O HIS 70 A O HIS 70 A N ILE 46 A N ILE 46 1 A ARG 8 0.311 SIDE CHAIN 1 A ARG 74 0.224 SIDE CHAIN 1 A ARG 76 0.280 SIDE CHAIN 1 A ARG 77 0.265 SIDE CHAIN 1 A ARG 78 0.244 SIDE CHAIN 2 A ARG 8 0.167 SIDE CHAIN 2 A ARG 35 0.301 SIDE CHAIN 2 A ARG 44 0.133 SIDE CHAIN 2 A ARG 74 0.275 SIDE CHAIN 2 A ARG 76 0.138 SIDE CHAIN 2 A ARG 77 0.292 SIDE CHAIN 2 A ARG 78 0.230 SIDE CHAIN 3 A ARG 8 0.295 SIDE CHAIN 3 A ARG 35 0.305 SIDE CHAIN 3 A ARG 44 0.299 SIDE CHAIN 3 A ARG 74 0.163 SIDE CHAIN 3 A ARG 76 0.140 SIDE CHAIN 3 A ARG 77 0.220 SIDE CHAIN 3 A ARG 78 0.310 SIDE CHAIN 4 A ARG 8 0.308 SIDE CHAIN 4 A ARG 35 0.309 SIDE CHAIN 4 A ARG 44 0.318 SIDE CHAIN 4 A ARG 74 0.304 SIDE CHAIN 4 A ARG 76 0.245 SIDE CHAIN 4 A ARG 77 0.318 SIDE CHAIN 4 A ARG 78 0.314 SIDE CHAIN 5 A ARG 8 0.318 SIDE CHAIN 5 A ARG 35 0.168 SIDE CHAIN 5 A ARG 44 0.299 SIDE CHAIN 5 A ARG 74 0.275 SIDE CHAIN 5 A ARG 76 0.301 SIDE CHAIN 5 A ARG 77 0.317 SIDE CHAIN 5 A ARG 78 0.276 SIDE CHAIN 6 A ARG 8 0.281 SIDE CHAIN 6 A ARG 35 0.297 SIDE CHAIN 6 A ARG 44 0.232 SIDE CHAIN 6 A ARG 74 0.310 SIDE CHAIN 6 A ARG 76 0.313 SIDE CHAIN 6 A ARG 77 0.210 SIDE CHAIN 6 A ARG 78 0.287 SIDE CHAIN 7 A ARG 8 0.289 SIDE CHAIN 7 A ARG 35 0.299 SIDE CHAIN 7 A ARG 44 0.310 SIDE CHAIN 7 A ARG 74 0.302 SIDE CHAIN 7 A ARG 76 0.140 SIDE CHAIN 7 A ARG 77 0.317 SIDE CHAIN 8 A ARG 8 0.271 SIDE CHAIN 8 A ARG 35 0.304 SIDE CHAIN 8 A ARG 44 0.228 SIDE CHAIN 8 A ARG 74 0.255 SIDE CHAIN 8 A ARG 76 0.298 SIDE CHAIN 8 A ARG 77 0.261 SIDE CHAIN 8 A ARG 78 0.316 SIDE CHAIN 9 A ARG 8 0.262 SIDE CHAIN 9 A ARG 35 0.278 SIDE CHAIN 9 A ARG 44 0.315 SIDE CHAIN 9 A ARG 74 0.282 SIDE CHAIN 9 A ARG 76 0.308 SIDE CHAIN 9 A ARG 77 0.254 SIDE CHAIN 9 A ARG 78 0.203 SIDE CHAIN 10 A ARG 8 0.292 SIDE CHAIN 10 A ARG 35 0.264 SIDE CHAIN 10 A ARG 44 0.091 SIDE CHAIN 10 A ARG 74 0.084 SIDE CHAIN 10 A ARG 76 0.219 SIDE CHAIN 10 A ARG 77 0.294 SIDE CHAIN 10 A ARG 78 0.202 SIDE CHAIN 9 -5.05 0.70 120.80 115.75 A A A CB CG CD2 PHE PHE PHE 9 9 9 N 1 A PHE 9 -68.89 96.64 1 A ASN 10 61.61 -131.31 1 A SER 12 77.60 -1.43 1 A SER 24 -60.84 -142.40 1 A ILE 25 -130.17 -31.11 1 A ALA 48 59.61 7.76 1 A ASP 62 103.78 30.63 1 A GLU 64 59.96 152.41 1 A GLN 66 74.60 106.40 1 A SER 67 -171.81 130.38 1 A ARG 74 -39.57 96.95 1 A ARG 77 -54.12 92.98 2 A ASN 10 62.12 -90.78 2 A SER 11 -128.35 -71.12 2 A SER 24 -61.24 -142.61 2 A ASP 62 155.02 36.61 2 A GLU 64 46.99 -154.34 2 A GLN 66 74.39 109.35 2 A SER 67 -175.87 129.84 2 A ARG 74 -53.64 108.35 2 A ARG 77 -53.70 92.28 3 A ASN 10 54.46 162.99 3 A SER 11 34.89 -109.21 3 A TYR 13 -48.12 153.74 3 A SER 24 69.31 -142.81 3 A ILE 25 -144.15 -25.50 3 A ASP 62 109.13 32.77 3 A GLU 64 51.60 -157.51 3 A GLN 66 80.23 111.54 3 A SER 67 -173.34 129.72 3 A ARG 77 -55.90 90.79 4 A ASN 10 61.62 -91.04 4 A SER 11 -165.30 -63.76 4 A TYR 13 -105.30 -160.92 4 A ILE 25 72.35 -30.57 4 A ALA 48 55.66 7.74 4 A ASP 62 103.26 37.45 4 A LEU 63 -66.60 -83.23 4 A GLU 64 76.45 162.26 4 A GLN 66 76.00 112.30 4 A SER 67 -163.18 118.58 4 A ARG 74 -48.24 105.02 4 A ARG 77 -56.42 92.33 5 A ASN 10 68.18 -84.62 5 A SER 11 -177.20 -32.09 5 A SER 24 65.78 -144.53 5 A ILE 25 -144.94 -28.26 5 A GLU 51 -48.36 88.75 5 A LEU 56 -42.47 162.74 5 A ASP 62 105.56 36.07 5 A GLU 64 62.94 144.33 5 A GLN 65 -37.14 135.83 5 A GLN 66 73.59 105.55 5 A ARG 74 -56.09 109.12 5 A ARG 77 -55.88 92.06 6 A ASN 10 66.77 -82.91 6 A SER 11 179.30 -31.54 6 A SER 24 -60.61 -135.98 6 A ILE 25 -135.81 -33.38 6 A ASP 62 106.56 31.16 6 A GLU 64 61.96 165.26 6 A GLN 66 75.27 108.23 6 A ARG 77 -55.94 91.83 7 A ASN 10 58.27 -92.39 7 A SER 11 -145.95 -83.34 7 A ILE 25 72.04 -35.07 7 A GLU 51 -48.48 96.88 7 A PRO 53 -72.81 -160.49 7 A ASP 62 90.49 33.72 7 A GLU 64 51.86 -154.61 7 A GLN 66 72.90 106.25 7 A SER 67 -175.41 131.93 7 A ARG 77 -56.47 91.66 8 A ASN 10 -32.86 150.57 8 A SER 11 79.47 -141.28 8 A ILE 25 72.16 -32.66 8 A ALA 48 59.41 9.61 8 A ASP 62 100.47 34.07 8 A GLU 64 60.31 151.28 8 A GLN 65 -33.89 127.51 8 A GLN 66 74.58 110.18 8 A ARG 77 -55.95 92.14 9 A ASN 10 -36.69 147.98 9 A SER 11 78.08 -145.06 9 A SER 24 -60.01 -131.56 9 A ILE 25 -139.69 -32.87 9 A ALA 48 59.35 7.33 9 A ASP 62 105.43 30.88 9 A GLU 64 56.87 163.59 9 A GLN 65 -37.85 122.84 9 A GLN 66 73.97 107.89 9 A ARG 74 -37.65 98.01 9 A ARG 77 -54.17 91.67 10 A ASN 10 -39.99 153.46 10 A SER 11 72.96 -151.06 10 A SER 24 -56.78 -149.02 10 A PRO 53 -77.75 -164.29 10 A ASP 62 107.12 31.88 10 A LEU 63 -72.90 -77.84 10 A GLU 64 71.24 159.47 10 A GLN 65 -37.99 122.62 10 A GLN 66 75.82 108.95 10 A ARG 74 -51.20 107.15 10 A ARG 77 -55.37 92.32 NMR structure of ubiquitin-like domain in murine Parkin 1 N N A ILE 25 A ILE 25 HELX_P A GLY 37 A GLY 37 1 1 13 APOPTOSIS parkinson disease, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, APOPTOSIS PRKN2_MOUSE UNP 1 1 Q9WVS6 MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRRR 1 76 1MG8 3 78 Q9WVS6 A 1 3 78 1 initiating methionine MET 1 1MG8 A Q9WVS6 UNP 1 1 cloning artifact GLY 2 1MG8 A Q9WVS6 UNP 2 4 anti-parallel parallel anti-parallel A GLY 14 A GLY 14 A GLU 18 A GLU 18 A ILE 4 A ILE 4 A ARG 8 A ARG 8 A ILE 68 A ILE 68 A ILE 71 A ILE 71 A VAL 45 A VAL 45 A PHE 47 A PHE 47