1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Zhao, C. Kigawa, T. Sato, M. Koshiba, S. Inoue, M. Yokoyama, S. 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 C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking To be Published 0353 Solution Structure of the Second UBA Domain in the Human Ubiquitin Specific Protease 5 (Isopeptidase 5) 10.2210/pdb2dak/pdb pdb_00002dak 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 6519.079 Ubiquitin carboxyl-terminal hydrolase 5 3.1.2.15 UBA domain 1 man polymer Ubiquitin thiolesterase 5, Ubiquitin-specific processing protease 5, Deubiquitinating enzyme 5, Isopeptidase T no no GSSGSSGPPEDCVTTIVSMGFSRDQALKALRATNNSLERAVDWIFSHIDDLDAEAAMSGPSSG GSSGSSGPPEDCVTTIVSMGFSRDQALKALRATNNSLERAVDWIFSHIDDLDAEAAMSGPSSG A hsi002005673.2 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 human Homo sample Cell-free protein synthesis USP5 9606 Homo sapiens Cell free synthesis PLASMID P050704-16 RIKEN Structural Genomics/Proteomics Initiative RSGI NPPSFA, National Project on Protein Structural and Functional Analyses database_2 pdbx_nmr_software pdbx_nmr_spectrometer pdbx_struct_assembly pdbx_struct_oper_list struct_ref_seq_dif repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2006-06-14 1 1 2008-04-30 1 2 2011-07-13 1 3 2022-03-09 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model _struct_ref_seq_dif.details Y PDBJ Y PDBJ 2005-12-14 REL target function, structures with the least restraint violations 100 20 3D_15N-separated_NOESY 3D_13C-separated_NOESY 120mM 7.0 ambient 296.0 K torsion angle dynamics, restrainted molecular dynamics 1 lowest energy 0.84mM UBA domain U-15N, 13C; 20mM d-Tris-HCl (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O 90% H2O/10% D2O Bruker Bruker collection XwinNMR 2.6 Delaglio, F. processing NMRPipe 20030801 Johnson, B. A. data analysis NMRView 5.0.4 Kobayashi, N. data analysis KUJIRA 0.9321 Guntert, P. structure solution CYANA 1.0.8 Guntert, P. refinement CYANA 1.0.8 700 Bruker AVANCE GLY 1 n 1 GLY 1 A SER 2 n 2 SER 2 A SER 3 n 3 SER 3 A GLY 4 n 4 GLY 4 A SER 5 n 5 SER 5 A SER 6 n 6 SER 6 A GLY 7 n 7 GLY 7 A PRO 8 n 8 PRO 8 A PRO 9 n 9 PRO 9 A GLU 10 n 10 GLU 10 A ASP 11 n 11 ASP 11 A CYS 12 n 12 CYS 12 A VAL 13 n 13 VAL 13 A THR 14 n 14 THR 14 A THR 15 n 15 THR 15 A ILE 16 n 16 ILE 16 A VAL 17 n 17 VAL 17 A SER 18 n 18 SER 18 A MET 19 n 19 MET 19 A GLY 20 n 20 GLY 20 A PHE 21 n 21 PHE 21 A SER 22 n 22 SER 22 A ARG 23 n 23 ARG 23 A ASP 24 n 24 ASP 24 A GLN 25 n 25 GLN 25 A ALA 26 n 26 ALA 26 A LEU 27 n 27 LEU 27 A LYS 28 n 28 LYS 28 A ALA 29 n 29 ALA 29 A LEU 30 n 30 LEU 30 A ARG 31 n 31 ARG 31 A ALA 32 n 32 ALA 32 A THR 33 n 33 THR 33 A ASN 34 n 34 ASN 34 A ASN 35 n 35 ASN 35 A SER 36 n 36 SER 36 A LEU 37 n 37 LEU 37 A GLU 38 n 38 GLU 38 A ARG 39 n 39 ARG 39 A ALA 40 n 40 ALA 40 A VAL 41 n 41 VAL 41 A ASP 42 n 42 ASP 42 A TRP 43 n 43 TRP 43 A ILE 44 n 44 ILE 44 A PHE 45 n 45 PHE 45 A SER 46 n 46 SER 46 A HIS 47 n 47 HIS 47 A ILE 48 n 48 ILE 48 A ASP 49 n 49 ASP 49 A ASP 50 n 50 ASP 50 A LEU 51 n 51 LEU 51 A ASP 52 n 52 ASP 52 A ALA 53 n 53 ALA 53 A GLU 54 n 54 GLU 54 A ALA 55 n 55 ALA 55 A ALA 56 n 56 ALA 56 A MET 57 n 57 MET 57 A SER 58 n 58 SER 58 A GLY 59 n 59 GLY 59 A PRO 60 n 60 PRO 60 A SER 61 n 61 SER 61 A SER 62 n 62 SER 62 A GLY 63 n 63 GLY 63 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 1 A A O H THR SER 14 18 1.54 1 A A O H GLN ALA 25 29 1.54 1 A A O H ARG TRP 39 43 1.56 2 A A O H THR SER 14 18 1.52 3 A A O H THR SER 14 18 1.51 3 A A O H GLN ALA 25 29 1.55 3 A A O H LEU ASN 30 35 1.58 4 A A O H THR SER 14 18 1.50 4 A A O H GLU THR 10 14 1.52 4 A A O H GLN ALA 25 29 1.55 4 A A O H LEU ASN 30 35 1.56 4 A A O H ARG TRP 39 43 1.57 4 A A O H LYS ALA 28 32 1.58 5 A A O H THR SER 14 18 1.51 5 A A O H GLN ALA 25 29 1.55 5 A A O H ARG TRP 39 43 1.56 6 A A O H THR SER 14 18 1.51 6 A A O H GLN ALA 25 29 1.56 6 A A O H ARG TRP 39 43 1.57 6 A A O H LYS ALA 28 32 1.58 7 A A O H THR SER 14 18 1.50 7 A A O H ASP LYS 24 28 1.52 7 A A O H ARG TRP 39 43 1.54 7 A A O H GLU THR 10 14 1.54 7 A A O H GLN ALA 25 29 1.58 7 A A O H LEU ASN 30 35 1.58 7 A A O H SER ALA 36 40 1.59 8 A A O H GLN ALA 25 29 1.54 8 A A O H ALA THR 29 33 1.58 9 A A O H THR SER 14 18 1.50 9 A A O H ALA THR 29 33 1.56 9 A A O H LYS ALA 28 32 1.57 9 A A O H ALA ILE 40 44 1.58 9 A A O H GLN ALA 25 29 1.59 10 A A O H GLN ALA 25 29 1.53 10 A A O H THR SER 14 18 1.57 10 A A O H ALA THR 29 33 1.57 11 A A O H THR SER 14 18 1.50 11 A A O H GLN ALA 25 29 1.51 11 A A O H ALA THR 29 33 1.57 12 A A O H THR SER 14 18 1.51 12 A A O H ARG TRP 39 43 1.53 12 A A O H LEU THR 30 33 1.56 12 A A O H ASP LYS 24 28 1.57 12 A A O H LEU ASN 30 35 1.58 12 A A O H GLN ALA 25 29 1.60 13 A A O H THR SER 14 18 1.54 13 A A O H GLU THR 10 14 1.55 13 A A O H ALA ILE 40 44 1.55 13 A A O H ALA THR 29 33 1.56 13 A A O H GLN ALA 25 29 1.58 14 A A O H THR SER 14 18 1.50 14 A A O H GLN ALA 25 29 1.55 14 A A O H ALA THR 29 33 1.57 15 A A O H GLU THR 10 14 1.51 15 A A O H GLN ALA 25 29 1.53 15 A A O H THR SER 14 18 1.53 15 A A O H ALA THR 29 33 1.56 15 A A O H SER ALA 36 40 1.59 15 A A O H LYS ALA 28 32 1.59 16 A A O H THR SER 14 18 1.50 16 A A O H GLN ALA 25 29 1.55 16 A A O H ALA THR 29 33 1.60 17 A A O H ASP LYS 24 28 1.50 17 A A O H THR SER 14 18 1.54 17 A A O H ARG TRP 39 43 1.55 17 A A O H LEU ASN 30 35 1.57 17 A A O H GLN ALA 25 29 1.58 18 A A O H THR SER 14 18 1.50 18 A A O H GLN ALA 25 29 1.54 18 A A O H LEU ASN 30 35 1.56 18 A A O H SER ALA 36 40 1.56 19 A A O H THR SER 14 18 1.50 19 A A O H LEU ASN 30 35 1.54 19 A A O H ARG TRP 39 43 1.55 19 A A O H GLN ALA 25 29 1.55 19 A A O H SER ALA 36 40 1.55 20 A A O H GLN ALA 25 29 1.53 20 A A O H THR SER 14 18 1.54 20 A A O H ASP LYS 24 28 1.57 20 A A O H ALA THR 29 33 1.58 20 A A O H ASP THR 11 15 1.59 1 A SER 3 -178.16 88.46 1 A SER 6 -47.79 160.22 1 A ASP 50 168.44 -38.01 1 A LEU 51 -67.73 78.76 1 A GLU 54 -41.63 157.48 1 A SER 61 -178.93 123.71 2 A SER 5 -179.94 -59.31 2 A SER 6 -152.00 83.02 2 A ASN 35 48.97 70.56 2 A ASP 52 -140.11 -55.52 2 A ALA 53 51.17 73.22 2 A ALA 56 -164.15 88.10 3 A SER 3 62.97 111.90 3 A SER 6 58.31 102.22 3 A THR 33 -102.30 45.35 3 A ASN 35 65.17 69.87 3 A ASP 50 -116.44 77.18 3 A ALA 53 -177.63 80.38 3 A GLU 54 73.64 -58.61 3 A ALA 55 51.31 97.71 3 A ALA 56 -161.56 112.50 3 A MET 57 58.44 87.30 4 A SER 5 -67.02 79.46 4 A THR 33 -88.99 40.16 4 A ASN 35 65.61 82.63 4 A ASP 50 179.89 106.96 4 A GLU 54 -165.18 113.45 4 A SER 61 -42.83 163.39 4 A SER 62 48.03 92.12 5 A ASN 35 61.49 66.66 5 A ASP 50 60.40 103.33 5 A ALA 55 51.25 97.37 5 A ALA 56 -64.91 91.86 5 A SER 61 56.48 108.00 5 A SER 62 178.36 147.67 6 A SER 5 -123.10 -58.51 6 A THR 33 -97.43 43.02 6 A ILE 44 -72.47 -70.98 6 A ASP 50 65.63 107.28 6 A ASP 52 49.45 94.00 6 A ALA 53 -161.77 63.26 6 A GLU 54 58.07 80.13 6 A SER 58 70.07 -62.80 6 A SER 62 59.74 152.41 7 A SER 3 -148.01 -59.45 7 A SER 6 59.73 152.56 7 A ASN 35 61.69 79.92 7 A ASP 49 -169.89 96.86 7 A ASP 52 60.18 109.00 7 A SER 61 -171.04 117.46 8 A SER 3 -160.41 -58.59 8 A SER 5 -122.68 -57.90 8 A THR 33 -89.03 40.19 8 A ASN 35 58.38 71.51 8 A ALA 53 -131.98 -46.28 8 A GLU 54 -173.06 81.84 8 A ALA 55 -166.50 -59.19 9 A SER 3 -162.16 99.94 9 A SER 5 -156.76 76.88 9 A SER 6 -143.05 -60.96 9 A ILE 16 -54.31 -71.71 9 A THR 33 -89.02 40.16 9 A ASN 35 40.46 80.02 9 A ILE 44 -54.46 -71.81 9 A LEU 51 -67.32 75.57 9 A ASP 52 71.33 112.02 9 A ALA 53 -175.15 74.27 9 A GLU 54 -39.24 111.70 9 A ALA 55 -169.81 81.21 9 A MET 57 -157.79 88.09 10 A SER 3 62.60 140.15 10 A SER 5 -150.57 -60.05 10 A SER 6 60.70 161.87 10 A THR 33 -93.89 42.42 10 A ASN 35 40.59 73.23 10 A ILE 44 -56.57 -70.13 10 A ASP 50 60.94 103.71 10 A ASP 52 -161.79 102.04 10 A ALA 53 -158.85 74.64 10 A ALA 55 -160.76 99.05 10 A ALA 56 46.75 78.46 10 A MET 57 -169.62 107.23 11 A SER 3 -39.95 141.29 11 A SER 5 53.28 83.40 11 A SER 6 60.53 86.18 11 A GLU 10 -90.40 -61.63 11 A ILE 16 -54.71 -71.71 11 A ASN 35 40.45 76.68 11 A ILE 44 -63.93 -70.06 11 A ASP 52 55.04 97.73 11 A ALA 53 -156.04 -45.87 11 A GLU 54 65.47 155.25 11 A ALA 55 62.51 77.40 12 A SER 5 -150.42 -61.47 12 A SER 6 66.06 96.58 12 A ASN 34 56.00 19.18 12 A ASN 35 79.78 62.92 12 A ILE 44 -71.01 -72.33 12 A ASP 50 173.17 113.19 12 A ASP 52 -124.53 -57.49 12 A GLU 54 -156.80 -59.87 12 A ALA 55 64.19 153.22 12 A ALA 56 42.47 79.15 12 A SER 61 -157.57 88.49 12 A SER 62 57.64 83.93 13 A SER 2 49.30 95.53 13 A GLU 10 -90.16 -62.90 13 A THR 33 -90.96 32.70 13 A ASN 35 42.45 79.41 13 A ILE 44 -56.10 -70.10 13 A ASP 50 67.07 110.23 13 A LEU 51 -104.17 -63.97 13 A ALA 53 -161.77 -44.45 13 A ALA 55 48.30 83.66 13 A MET 57 56.99 109.65 13 A SER 62 -175.02 126.54 14 A SER 2 57.30 92.47 14 A SER 3 57.89 96.07 14 A ILE 16 -57.18 -71.35 14 A THR 33 -93.79 42.42 14 A ASP 50 -138.70 -47.25 14 A ASP 52 42.70 86.83 14 A GLU 54 68.79 148.63 14 A ALA 55 -64.71 88.83 14 A ALA 56 -166.40 62.05 15 A SER 2 62.64 159.18 15 A SER 3 -174.19 -58.50 15 A ASN 34 44.12 73.12 15 A ASN 35 40.47 83.44 15 A ASP 50 -160.62 99.94 15 A ASP 52 55.15 101.52 15 A ALA 56 -173.88 102.24 15 A SER 62 -43.55 107.80 16 A SER 2 -162.06 110.22 16 A SER 6 -142.39 -59.63 16 A CYS 12 -50.24 -70.01 16 A THR 33 -97.36 44.31 16 A ILE 44 -64.80 -70.64 16 A ASP 49 -100.01 69.82 16 A ASP 50 -169.58 69.55 16 A LEU 51 38.33 87.21 16 A ASP 52 -171.67 92.37 16 A GLU 54 -107.88 53.45 16 A ALA 56 -58.14 171.83 16 A SER 62 -170.65 82.49 17 A SER 2 179.61 145.46 17 A ASN 34 40.49 29.90 17 A ASN 35 70.11 66.57 17 A HIS 47 -90.79 45.47 17 A ASP 49 70.26 -61.02 17 A ASP 50 178.37 100.88 17 A ASP 52 -152.02 -56.29 17 A ALA 55 -133.17 -62.00 17 A ALA 56 58.94 78.67 17 A SER 62 63.13 106.92 18 A ILE 16 -59.33 -72.41 18 A THR 33 -95.51 43.03 18 A ASN 35 67.89 71.10 18 A ILE 44 -62.67 -71.26 18 A LEU 51 -102.29 69.30 18 A ASP 52 -179.06 128.36 18 A GLU 54 48.75 97.30 18 A ALA 56 63.18 106.31 19 A SER 3 67.17 -72.34 19 A SER 6 65.94 153.06 19 A THR 33 -89.81 39.39 19 A ASN 35 67.72 70.55 19 A HIS 47 -91.58 43.76 19 A ASP 52 44.66 91.27 20 A SER 3 -176.50 128.74 20 A SER 5 64.38 88.61 20 A SER 6 -155.70 -58.63 20 A THR 33 -96.21 43.61 20 A ASN 35 40.21 70.71 20 A LEU 51 38.36 78.82 20 A ASP 52 174.44 118.90 20 A ALA 55 61.66 168.82 Solution Structure of the Second UBA Domain in the Human Ubiquitin Specific Protease 5 (Isopeptidase 5) 1 N N A PRO 9 A PRO 9 HELX_P A GLY 20 A GLY 20 1 1 12 A SER 22 A SER 22 HELX_P A THR 33 A THR 33 1 2 12 A LEU 37 A LEU 37 HELX_P A ASP 50 A ASP 50 1 3 14 HYDROLASE isopeptidase T, Ubiquitin Specific Protease 5, USP 5, UBA domain, structural genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, HYDROLASE UBP5_HUMAN UNP 1 723 P45974 723 772 2DAK 8 57 P45974 A 1 8 57 1 cloning artifact GLY 1 2DAK A P45974 UNP 1 1 cloning artifact SER 2 2DAK A P45974 UNP 2 1 cloning artifact SER 3 2DAK A P45974 UNP 3 1 cloning artifact GLY 4 2DAK A P45974 UNP 4 1 cloning artifact SER 5 2DAK A P45974 UNP 5 1 cloning artifact SER 6 2DAK A P45974 UNP 6 1 cloning artifact GLY 7 2DAK A P45974 UNP 7 1 cloning artifact SER 58 2DAK A P45974 UNP 58 1 cloning artifact GLY 59 2DAK A P45974 UNP 59 1 cloning artifact PRO 60 2DAK A P45974 UNP 60 1 cloning artifact SER 61 2DAK A P45974 UNP 61 1 cloning artifact SER 62 2DAK A P45974 UNP 62 1 cloning artifact GLY 63 2DAK A P45974 UNP 63