1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Fu, Q.S. Zhou, C.J. Gao, H.C. Lin, D.H. Hu, H.Y. 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 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 C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US J.Biol.Chem. JBCHA3 0071 0021-9258 284 19043 19052 10.1074/jbc.M109.009126 19423704 Structural Basis for Ubiquitin Recognition by a Novel Domain from Human Phospholipase A2-activating Protein. 2009 10.2210/pdb2k8c/pdb pdb_00002k8c 8576.831 Ubiquitin 1 man polymer 9032.011 Phospholipase A-2-activating protein UNP residues 386-465 1 man polymer PLA2P, PLAP no no MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG A polypeptide(L) no no ANQQTSGKVLYEGKEFDYVFSIDVNEGGPSYKLPYNTSDDPWLTAYNFLQKNDLNPMFLDQVAKFIIDNTKGQMLGLGNP ANQQTSGKVLYEGKEFDYVFSIDVNEGGPSYKLPYNTSDDPWLTAYNFLQKNDLNPMFLDQVAKFIIDNTKGQMLGLGNP 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 n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n 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 RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC 9606 Homo sapiens 562 Escherichia coli BL21(DE3) pET-22B Human sample PLAA, PLAP 9606 Homo sapiens 562 Escherichia coli BL21(DE3) pET-32M database_2 pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Database references Derived calculations 1 0 2009-05-05 1 1 2011-07-13 1 2 2022-03-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession Solution structure of Ubiquitin-binding domain PLAA (PFUC, Gly76-Pro77 cis isomer) Solution structure of Ubiquitin-binding domain PLAA (PFUC, Gly76-Pro77 trans isomer) Solution structure of PLAA family ubiquitin binding domain (PFUC) cis isomer in complex with ubiquitin BMRB Y RCSB 2008-09-04 REL REL 10 structures for lowest energy 200 10 2D 1H-15N HSQC 2D 1H-15N HSQC 0.2 mM [U-100% 15N] 0.2 mM [U-100% 15N] 50mM NaCl 6.5 ambient 298 K The structures were calculated with HADDOCK by NMR restraint-guided docking simulated annealing 1 lowest energy 0.2 mM [U-100% 15N] Ubiquitin, 90% H2O, 10% D2O 90% H2O/10% D2O 0.2 mM [U-100% 15N] PFUC_trans, 90% H2O, 10% D2O 90% H2O/10% D2O Brunger, Adams, Clore, Gros, Nilges and Read refinement CNS 600 Varian UNITY Varian Unity 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 ARG 74 n 74 ARG 74 A GLY 75 n 75 GLY 75 A GLY 76 n 76 GLY 76 A ALA 49 n 1 ALA 49 B ASN 50 n 2 ASN 50 B GLN 51 n 3 GLN 51 B GLN 52 n 4 GLN 52 B THR 53 n 5 THR 53 B SER 54 n 6 SER 54 B GLY 55 n 7 GLY 55 B LYS 56 n 8 LYS 56 B VAL 57 n 9 VAL 57 B LEU 58 n 10 LEU 58 B TYR 59 n 11 TYR 59 B GLU 60 n 12 GLU 60 B GLY 61 n 13 GLY 61 B LYS 62 n 14 LYS 62 B GLU 63 n 15 GLU 63 B PHE 64 n 16 PHE 64 B ASP 65 n 17 ASP 65 B TYR 66 n 18 TYR 66 B VAL 67 n 19 VAL 67 B PHE 68 n 20 PHE 68 B SER 69 n 21 SER 69 B ILE 70 n 22 ILE 70 B ASP 71 n 23 ASP 71 B VAL 72 n 24 VAL 72 B ASN 73 n 25 ASN 73 B GLU 74 n 26 GLU 74 B GLY 75 n 27 GLY 75 B GLY 76 n 28 GLY 76 B PRO 77 n 29 PRO 77 B SER 78 n 30 SER 78 B TYR 79 n 31 TYR 79 B LYS 80 n 32 LYS 80 B LEU 81 n 33 LEU 81 B PRO 82 n 34 PRO 82 B TYR 83 n 35 TYR 83 B ASN 84 n 36 ASN 84 B THR 85 n 37 THR 85 B SER 86 n 38 SER 86 B ASP 87 n 39 ASP 87 B ASP 88 n 40 ASP 88 B PRO 89 n 41 PRO 89 B TRP 90 n 42 TRP 90 B LEU 91 n 43 LEU 91 B THR 92 n 44 THR 92 B ALA 93 n 45 ALA 93 B TYR 94 n 46 TYR 94 B ASN 95 n 47 ASN 95 B PHE 96 n 48 PHE 96 B LEU 97 n 49 LEU 97 B GLN 98 n 50 GLN 98 B LYS 99 n 51 LYS 99 B ASN 100 n 52 ASN 100 B ASP 101 n 53 ASP 101 B LEU 102 n 54 LEU 102 B ASN 103 n 55 ASN 103 B PRO 104 n 56 PRO 104 B MET 105 n 57 MET 105 B PHE 106 n 58 PHE 106 B LEU 107 n 59 LEU 107 B ASP 108 n 60 ASP 108 B GLN 109 n 61 GLN 109 B VAL 110 n 62 VAL 110 B ALA 111 n 63 ALA 111 B LYS 112 n 64 LYS 112 B PHE 113 n 65 PHE 113 B ILE 114 n 66 ILE 114 B ILE 115 n 67 ILE 115 B ASP 116 n 68 ASP 116 B ASN 117 n 69 ASN 117 B THR 118 n 70 THR 118 B LYS 119 n 71 LYS 119 B GLY 120 n 72 GLY 120 B GLN 121 n 73 GLN 121 B MET 122 n 74 MET 122 B LEU 123 n 75 LEU 123 B GLY 124 n 76 GLY 124 B LEU 125 n 77 LEU 125 B GLY 126 n 78 GLY 126 B ASN 127 n 79 ASN 127 B PRO 128 n 80 PRO 128 B author_defined_assembly 2 dimeric 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 LYS 6 A N LYS 6 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 N TYR 59 B N TYR 11 B O LYS 62 B O LYS 14 B N TYR 66 B N TYR 18 B O TYR 83 B O TYR 35 1 B B HZ3 OD1 LYS ASP 56 65 1.55 1 B B OD1 HZ1 ASP LYS 108 112 1.56 1 A B HZ3 OD2 LYS ASP 6 71 1.59 1 A A OE1 HZ3 GLU LYS 16 33 1.59 2 B B OD1 HZ1 ASP LYS 108 112 1.55 2 B B HZ1 OD1 LYS ASP 56 65 1.58 3 B B HZ1 OD1 LYS ASP 56 65 1.54 4 B B HZ1 OD1 LYS ASP 56 65 1.54 4 B B OE2 HZ1 GLU LYS 60 99 1.56 5 A B HZ3 OD2 LYS ASP 6 71 1.59 5 A B HE2 OD1 HIS ASP 68 71 1.60 6 B B HZ1 OD1 LYS ASP 56 65 1.56 6 B B OE2 HZ1 GLU LYS 60 99 1.59 6 A B HE2 OD1 HIS ASP 68 71 1.59 6 A B HZ3 OD2 LYS ASP 6 71 1.59 6 A A HZ3 OD1 LYS ASP 27 52 1.60 8 A B HZ3 OD2 LYS ASP 6 71 1.58 8 A B HE2 OD1 HIS ASP 68 71 1.60 9 B B OD1 HZ1 ASP LYS 108 112 1.56 9 A A OE2 HZ3 GLU LYS 16 33 1.57 9 B B OE2 HZ1 GLU LYS 60 99 1.59 9 B B HZ1 OD1 LYS ASP 56 65 1.60 10 B B HZ1 OD1 LYS ASP 56 65 1.55 10 B B OD2 HZ1 ASP LYS 108 112 1.56 10 A B HE2 OD2 HIS ASP 68 71 1.60 10 B B OE2 HZ2 GLU LYS 60 99 1.60 1 A LYS 33 -79.06 -71.26 1 A LEU 71 -109.08 -159.65 1 B GLN 51 -130.24 -50.56 1 B THR 53 -79.48 38.22 1 B ASP 65 -71.12 -70.30 1 B THR 85 -74.08 24.47 1 B SER 86 -151.30 30.10 1 B ASP 101 63.40 91.57 1 B LYS 119 -108.11 -89.17 1 B LEU 123 -88.81 -84.59 2 A PRO 38 -69.83 0.63 2 A ALA 46 65.83 -73.52 2 A LEU 71 -102.49 -101.93 2 A ARG 74 -124.58 -83.69 2 B ASN 50 63.37 70.88 2 B SER 54 -96.78 -85.11 2 B ASP 65 -69.17 -80.89 2 B VAL 72 -166.29 -38.03 2 B ASP 101 55.74 74.62 2 B LYS 119 -127.14 -50.15 2 B LEU 125 61.40 -90.54 3 A LEU 71 -96.13 -97.10 3 B ASN 50 64.61 68.49 3 B ASP 65 -69.91 -79.01 3 B VAL 72 177.10 -30.51 3 B ASP 101 58.86 82.19 3 B LEU 125 64.32 -95.40 4 A LYS 33 -81.13 -76.51 4 A ALA 46 68.10 -12.54 4 B SER 54 -100.05 -77.84 4 B GLU 60 59.08 19.50 4 B ASP 65 -72.14 -84.09 4 B VAL 72 -175.26 -38.87 4 B SER 86 -105.75 50.86 4 B ASP 101 60.92 67.79 4 B LYS 119 -122.81 -51.93 4 B LEU 125 67.91 -80.10 5 A LEU 71 -92.17 -137.95 5 B ASP 101 58.72 87.86 5 B LYS 119 -95.74 -103.86 5 B LEU 123 -100.00 -81.08 6 A GLU 34 -99.15 -74.01 6 A ALA 46 62.15 -83.66 6 B ASN 50 58.80 81.61 6 B SER 54 -101.88 -75.38 6 B ASP 65 -65.49 -76.15 6 B VAL 72 179.43 -25.41 6 B LEU 125 66.06 -86.26 7 A GLN 62 -120.63 -168.92 7 A ARG 74 -112.00 -168.61 7 B THR 53 -95.23 45.51 7 B SER 54 -81.53 -72.23 7 B ASP 65 -70.31 -84.23 7 B VAL 72 178.33 -25.70 7 B LYS 119 -138.82 -56.52 7 B LEU 125 67.02 -80.39 8 B LYS 119 -89.40 -74.23 8 B LEU 123 -94.57 -79.71 9 A LEU 71 -102.18 -153.38 9 B ASN 50 60.20 61.89 9 B THR 53 -96.08 46.56 9 B PHE 64 -118.41 -169.31 9 B ASP 65 -65.76 -85.72 9 B VAL 72 -177.40 -41.88 9 B SER 86 -106.28 41.81 9 B ASP 101 60.27 76.61 9 B LYS 119 -121.23 -52.72 9 B GLN 121 -138.23 -41.72 9 B LEU 125 65.41 -87.37 10 B SER 54 -106.73 -87.22 10 B ASP 65 -70.76 -86.23 10 B VAL 72 -175.99 -28.94 10 B ASP 101 60.29 81.70 10 B GLN 121 -135.54 -55.27 10 B LEU 125 62.14 -93.75 Solution structure of PLAA family ubiquitin binding domain (PFUC) trans isomer in complex with ubiquitin 1 N N 2 N N A THR 22 A THR 22 HELX_P A GLU 34 A GLU 34 1 1 13 B ASP 88 B ASP 40 HELX_P B GLN 98 B GLN 50 1 2 11 B PRO 104 B PRO 56 HELX_P B THR 118 B THR 70 1 3 15 PROTEIN BINDING Ubiquitin in complex with PFUC trans isomer, Cytoplasm, Nucleus, Phosphoprotein, Ubl conjugation, WD repeat, PROTEIN BINDING UBIQ_HUMAN UNP 1 1 P62988 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG PLAP_HUMAN UNP 2 386 Q9Y263 ANQQTSGKVLYEGKEFDYVFSIDVNEGGPSYKLPYNTSDDPWLTAYNFLQKNDLNPMFLDQVAKFIIDNTKGQMLGLGNP 1 76 2K8C 1 76 P62988 A 1 1 76 386 465 2K8C 49 128 Q9Y263 B 2 1 80 5 2 2 anti-parallel parallel anti-parallel anti-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 VAL 70 A VAL 70 A ARG 42 A ARG 42 A PHE 45 A PHE 45 A LYS 48 A LYS 48 A GLN 49 A GLN 49 B VAL 57 B VAL 9 B TYR 59 B TYR 11 B LYS 62 B LYS 14 B PHE 64 B PHE 16 B TYR 66 B TYR 18 B ILE 70 B ILE 22 B TYR 79 B TYR 31 B TYR 83 B TYR 35