1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Skelton, N.J. Koehler, M.F.T. Zobel, K. Wong, W.L. Yeh, S. Pisabarro, M.T. Yin, J.P. Lasky, L.A. Sidhu, S.S. 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 278 7645 7654 10.1074/jbc.M209751200 12446668 Origins of PDZ domain ligand specificity. Structure determination and mutagenesis of the Erbin PDZ domain. 2003 10.2210/pdb1n7t/pdb pdb_00001n7t 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 11196.597 99-mer peptide of densin-180-like protein Erbin pdz domain 1 man polymer the peptide is related to the C-termini of the p120-like catenins. 877.939 phage-derived peptide 1 syn polymer no no GSHMGHELAKQEIRVRVEKDPELGFSISGGVGGRGNPFRPDDDGIFVTRVQPEGPASKLLQPGDKIIQANGYSFINIEHG QAVSLLKTFQNTVELIIVREVSS GSHMGHELAKQEIRVRVEKDPELGFSISGGVGGRGNPFRPDDDGIFVTRVQPEGPASKLLQPGDKIIQANGYSFINIEHG QAVSLLKTFQNTVELIIVREVSS A polypeptide(L) no no TGWETWV TGWETWV 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 human Homo Escherichia Escherichia coli sample erbin 9606 Homo sapiens 511693 Escherichia coli BL21 BL21 plasmid pET15b database_2 pdbx_nmr_software 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 2003-01-28 1 1 2008-04-28 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_ref_seq_dif.details SEQUENCE The phage-derived peptide, chain B, is de novo design. No sequence database reference is available for the peptide. RCSB Y RCSB 2002-11-16 REL REL THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. IT WAS selected from A phage display library. sample The resonance assignments were determined using triple-resonance NMR spectroscopy. least violation of experimental restraints 100 20 3D_15N-separated_NOESY HNHA 3D HNHB 3D 15N-separated low mixing time TOCSY 2D-15N-filtered NOESY 3D_13C-separated_NOESY 3D-13_filtered, 13C-edited NOESY 2D-13C-filtered NOESY 250 mM 6.5 1 atm 298 K 250 mM 6.5 1 atm 298 K 250 mM 6.5 1 atm 298 K 250 mM 6.5 1 atm 298 K The complex was determined using a total of 1717 NOE distance restraints (148 intra residue, 339 sequential, 328 medium range, 699 long-range and 203 intermolecular), 36 hydrogen bond restraints, 156 dihedral angle restraints (86 phi, 44 psi and 26 chi-1) and 82 15N residual dipolar coupling restraints. The best 20 conformers (of 100) had no distance violations greater than 0.12A and no dihedral angle violations greater than 3.0 degrees. RMSD from experimental distance restraints was 0.0055+/-0.0007. The mean backbone rmsd from the mean structure was 0.40+/- 0.05 A for N, Ca and C atoms of residues 10-100. 74% (25%) of residues were in the most favoured (allowed) region of phi/psi space; no residues were in the disallowed region. torsion angle dynamics, simulated annealing 2 closest to the average 2 mM Erbin PDZ (15N) + 2.2 mM peptide; 25 mM sodium phosphate pH 6.5; 50 mM sodium chloride 90% H2O, 10% D20 2 mM Erbin PDZ (15N,13C) + 2.2 mM peptide; 25 mM sodium phosphate pH 6.5; 50 mM sodium chloride 90% H2O, 10% D20 2 mM Erbin PDZ (15N,13C) + 2.2 mM peptide; 25 mM sodium phosphate pH 6.5; 50 mM sodium chloride 100% D2O 2 mM Erbin PDZ (15N) + 2.2 mM peptide; 25 mM sodium phosphate pH 6.5; 50 mM sodium chloride; 15 mg/ml Pf1 phage 90% H2O, 10% D20 bruker collection XwinNMR 3.1 Accelrys data analysis Felix 98 Accelrys refinement CNS 2000.1 600 Bruker DRX 800 Bruker DRX GLY 1 n 1 GLY 1 A SER 2 n 2 SER 2 A HIS 3 n 3 HIS 3 A MET 4 n 4 MET 4 A GLY 5 n 5 GLY 5 A HIS 6 n 6 HIS 6 A GLU 7 n 7 GLU 7 A LEU 8 n 8 LEU 8 A ALA 9 n 9 ALA 9 A LYS 10 n 10 LYS 10 A GLN 11 n 11 GLN 11 A GLU 12 n 12 GLU 12 A ILE 13 n 13 ILE 13 A ARG 14 n 14 ARG 14 A VAL 15 n 15 VAL 15 A ARG 16 n 16 ARG 16 A VAL 17 n 17 VAL 17 A GLU 18 n 18 GLU 18 A LYS 19 n 19 LYS 19 A ASP 20 n 20 ASP 20 A PRO 21 n 21 PRO 21 A GLU 22 n 22 GLU 22 A LEU 23 n 23 LEU 23 A GLY 24 n 24 GLY 24 A PHE 25 n 25 PHE 25 A SER 26 n 26 SER 26 A ILE 27 n 27 ILE 27 A SER 28 n 28 SER 28 A GLY 29 n 29 GLY 29 A GLY 30 n 30 GLY 30 A VAL 31 n 31 VAL 31 A GLY 32 n 32 GLY 32 A GLY 33 n 33 GLY 33 A ARG 34 n 34 ARG 34 A GLY 35 n 35 GLY 35 A ASN 36 n 36 ASN 36 A PRO 37 n 37 PRO 37 A PHE 38 n 38 PHE 38 A ARG 39 n 39 ARG 39 A PRO 40 n 40 PRO 40 A ASP 41 n 41 ASP 41 A ASP 42 n 42 ASP 42 A ASP 43 n 43 ASP 43 A GLY 44 n 44 GLY 44 A ILE 45 n 45 ILE 45 A PHE 46 n 46 PHE 46 A VAL 47 n 47 VAL 47 A THR 48 n 48 THR 48 A ARG 49 n 49 ARG 49 A VAL 50 n 50 VAL 50 A GLN 51 n 51 GLN 51 A PRO 52 n 52 PRO 52 A GLU 53 n 53 GLU 53 A GLY 54 n 54 GLY 54 A PRO 55 n 55 PRO 55 A ALA 56 n 56 ALA 56 A SER 57 n 57 SER 57 A LYS 58 n 58 LYS 58 A LEU 59 n 59 LEU 59 A LEU 60 n 60 LEU 60 A GLN 61 n 61 GLN 61 A PRO 62 n 62 PRO 62 A GLY 63 n 63 GLY 63 A ASP 64 n 64 ASP 64 A LYS 65 n 65 LYS 65 A ILE 66 n 66 ILE 66 A ILE 67 n 67 ILE 67 A GLN 68 n 68 GLN 68 A ALA 69 n 69 ALA 69 A ASN 70 n 70 ASN 70 A GLY 71 n 71 GLY 71 A TYR 72 n 72 TYR 72 A SER 73 n 73 SER 73 A PHE 74 n 74 PHE 74 A ILE 75 n 75 ILE 75 A ASN 76 n 76 ASN 76 A ILE 77 n 77 ILE 77 A GLU 78 n 78 GLU 78 A HIS 79 n 79 HIS 79 A GLY 80 n 80 GLY 80 A GLN 81 n 81 GLN 81 A ALA 82 n 82 ALA 82 A VAL 83 n 83 VAL 83 A SER 84 n 84 SER 84 A LEU 85 n 85 LEU 85 A LEU 86 n 86 LEU 86 A LYS 87 n 87 LYS 87 A THR 88 n 88 THR 88 A PHE 89 n 89 PHE 89 A GLN 90 n 90 GLN 90 A ASN 91 n 91 ASN 91 A THR 92 n 92 THR 92 A VAL 93 n 93 VAL 93 A GLU 94 n 94 GLU 94 A LEU 95 n 95 LEU 95 A ILE 96 n 96 ILE 96 A ILE 97 n 97 ILE 97 A VAL 98 n 98 VAL 98 A ARG 99 n 99 ARG 99 A GLU 100 n 100 GLU 100 A VAL 101 n 101 VAL 101 A SER 102 n 102 SER 102 A SER 103 n 103 SER 103 A THR 301 n 1 THR 301 B GLY 302 n 2 GLY 302 B TRP 303 n 3 TRP 303 B GLU 304 n 4 GLU 304 B THR 305 n 5 THR 305 B TRP 306 n 6 TRP 306 B VAL 307 n 7 VAL 307 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 N VAL 15 A N VAL 15 A O LEU 95 A O LEU 95 A O ILE 96 A O ILE 96 A N GLN 68 A N GLN 68 A N ALA 69 A N ALA 69 A O TYR 72 A O TYR 72 A O PHE 46 A O PHE 46 A N SER 28 A N SER 28 A N ILE 27 A N ILE 27 B O THR 305 B O THR 5 1 A ALA 9 -171.00 -171.17 1 A ASP 20 -166.98 89.06 1 A PRO 37 -92.85 34.90 1 A GLN 51 -103.91 -68.09 1 A PRO 55 -60.20 -70.03 1 A ALA 56 -99.02 43.40 1 A LEU 59 -91.62 -69.52 1 A ASN 70 46.47 29.00 1 A GLN 90 -65.65 -137.75 1 B TRP 303 -169.89 -42.25 2 A SER 2 -162.44 -47.28 2 A ALA 9 -144.48 44.20 2 A LYS 10 -174.65 -179.27 2 A ASP 20 -175.29 84.02 2 A GLN 51 -102.66 -67.89 2 A PRO 55 -58.26 -76.43 2 A SER 57 -107.35 -67.25 2 A ASN 76 61.23 62.36 2 A PHE 89 -48.98 172.70 2 A GLN 90 -84.31 -143.46 3 A ALA 9 -102.14 -158.43 3 A ASP 20 -173.97 85.52 3 A GLN 51 -102.86 -69.95 3 A LEU 59 -92.23 -65.11 3 A GLN 90 -62.59 -131.40 3 A ASN 91 -82.59 -72.28 4 A GLU 7 -113.90 66.80 4 A ALA 9 -102.25 47.88 4 A ASP 20 -175.10 84.87 4 A ASN 36 -173.54 142.30 4 A PRO 37 -90.42 39.87 4 A PHE 38 -125.62 -53.44 4 A GLN 51 -97.13 -70.41 4 A LEU 59 -92.04 -72.61 4 A ASN 76 62.54 73.78 4 A PHE 89 -47.87 172.81 4 A GLN 90 -92.50 -138.00 4 A ASN 91 -78.96 -74.97 5 A LEU 8 -106.79 -84.74 5 A ALA 9 -174.96 35.58 5 A ASP 20 -163.59 86.87 5 A ASN 36 -170.74 132.69 5 A PRO 37 -91.52 44.15 5 A PHE 38 -122.84 -57.77 5 A GLN 51 -104.87 -68.17 5 A PRO 55 -57.05 -76.11 5 A SER 57 -99.73 -63.27 5 A PRO 62 -63.79 79.06 5 A ASP 64 -96.24 -158.25 5 A ASN 70 46.72 29.27 5 A GLN 90 -66.72 -136.60 6 A ASP 20 -171.11 88.22 6 A ASP 43 -100.03 64.62 6 A GLN 51 -104.97 -68.45 6 A PRO 55 -58.89 -76.82 6 A SER 57 -105.04 -67.45 6 A PRO 62 -68.80 73.79 6 A ASN 70 46.47 29.77 6 A ASN 76 62.81 75.77 6 A PHE 89 -46.67 170.85 6 A GLN 90 -88.56 -142.23 6 B TRP 303 -161.68 -43.94 7 A LEU 8 -97.39 -63.10 7 A LYS 10 -172.78 117.86 7 A PHE 38 -133.92 -51.37 7 A GLN 51 -104.38 -67.82 7 A PRO 55 -59.57 -74.45 7 A ALA 56 -106.90 46.76 7 A SER 57 -108.54 -60.39 7 A LEU 59 -93.23 -63.35 7 A ASN 76 64.24 74.17 7 A PHE 89 -45.56 170.99 7 A GLN 90 -84.56 -143.01 7 B TRP 303 -162.52 -158.97 7 B GLU 304 -69.54 -179.64 8 A HIS 3 -57.79 108.22 8 A GLU 7 -125.56 -159.21 8 A LEU 8 -56.42 109.97 8 A ALA 9 -151.92 -144.28 8 A LYS 10 -43.88 108.05 8 A ASP 20 -173.75 83.45 8 A ASP 43 -102.18 40.82 8 A GLN 51 -104.55 -68.71 8 A PRO 55 -58.59 -71.93 8 A ALA 56 -105.87 47.34 8 A LEU 59 -92.60 -64.87 8 A PHE 89 -46.74 170.90 8 A GLN 90 -83.85 -142.85 8 A ASN 91 -79.48 -70.30 9 A ALA 9 -103.34 61.80 9 A ASP 20 -175.85 81.39 9 A ARG 34 -173.12 -42.22 9 A ASP 43 -106.79 66.70 9 A GLN 51 -105.54 -68.99 9 A PRO 55 -58.63 -78.06 9 A ALA 56 -117.06 53.96 9 A SER 57 -108.14 -65.12 9 A ASN 76 61.87 74.88 9 A GLN 90 -65.18 -136.65 9 A ASN 91 -80.30 -70.36 10 A SER 2 -152.04 -63.32 10 A MET 4 -141.17 -47.55 10 A HIS 6 -157.99 -48.35 10 A ALA 9 -169.29 -161.34 10 A ASP 20 -174.65 82.72 10 A GLN 51 -102.10 -69.67 10 A PRO 55 -59.70 -77.49 10 A ALA 56 -106.80 49.57 10 A SER 57 -100.86 -61.41 10 A ASN 70 45.62 28.18 10 A PHE 89 -47.54 171.38 10 A GLN 90 -77.53 -145.60 11 A SER 2 -148.86 33.31 11 A GLU 7 -68.80 -174.24 11 A LYS 10 -174.89 125.46 11 A ASP 20 -172.84 85.70 11 A GLN 51 -104.99 -67.92 11 A PRO 55 -60.98 -75.41 11 A ALA 56 -108.15 47.52 11 A ASN 76 61.09 70.82 11 A ASN 91 -134.60 -81.95 12 A LEU 8 -144.63 35.73 12 A ALA 9 -88.98 -146.09 12 A LYS 10 -44.20 107.79 12 A ASP 20 -169.37 86.89 12 A ASP 41 -155.41 18.91 12 A ASP 43 -89.61 40.64 12 A GLN 51 -96.02 -68.07 12 A PRO 55 -57.96 -73.74 12 A ASN 76 61.46 70.41 12 A PHE 89 -49.09 173.66 12 A GLN 90 -87.84 -140.25 12 A SER 102 -162.42 102.01 12 B TRP 303 -147.67 20.73 13 A HIS 6 -147.77 -72.33 13 A ASP 20 -174.95 83.35 13 A PRO 37 -93.42 34.19 13 A GLN 51 -102.77 -71.34 13 A ALA 56 -108.56 45.25 13 A LEU 59 -95.48 -65.34 13 A ASP 64 -67.77 -177.66 13 A ASN 76 63.18 72.75 13 A PHE 89 -46.88 174.70 13 A GLN 90 -85.79 -143.69 13 A ASN 91 -81.15 -70.71 13 B TRP 303 -165.28 -42.04 14 A GLU 7 -141.78 28.60 14 A ASP 20 -175.89 78.12 14 A ARG 34 -178.35 -77.29 14 A ASP 43 -108.44 42.39 14 A GLN 51 -105.31 -68.24 14 A PRO 55 -59.67 -74.46 14 A LEU 59 -91.24 -65.14 14 A ASN 76 62.17 76.47 14 A GLN 90 -63.29 -139.31 15 A MET 4 -90.00 -62.89 15 A LYS 19 -105.70 74.95 15 A VAL 31 -151.40 81.38 15 A GLN 51 -105.25 -68.81 15 A ASN 70 45.13 27.64 15 A ASN 76 61.11 76.86 15 A PHE 89 -51.06 176.40 15 A GLN 90 -82.08 -144.00 16 A LEU 8 -170.83 -41.71 16 A ALA 9 -64.17 -160.05 16 A LYS 10 -51.46 102.86 16 A LYS 19 -112.30 73.28 16 A ASN 36 -173.89 132.86 16 A ASP 43 -102.30 64.52 16 A GLN 51 -104.73 -68.30 16 A PRO 55 -58.57 -72.52 16 A PRO 62 -64.15 71.16 16 A ASN 76 62.13 75.93 16 A PHE 89 -49.74 177.02 16 A GLN 90 -82.17 -144.83 17 A ASP 20 -171.98 85.57 17 A PRO 37 -92.33 30.32 17 A ASP 43 -98.88 54.82 17 A GLN 51 -105.06 -68.85 17 A PRO 55 -60.07 -75.81 17 A ALA 56 -104.05 46.06 17 A ASN 70 42.56 28.87 17 A ASN 76 61.29 73.78 17 A PHE 89 -47.82 173.55 17 A GLN 90 -81.38 -145.58 18 A SER 2 -160.44 33.08 18 A HIS 6 -165.56 33.70 18 A GLN 51 -104.86 -68.23 18 A PRO 55 -58.32 -76.44 18 A ALA 56 -115.32 50.95 18 A ASN 76 63.30 76.17 18 A GLN 90 -65.77 -105.34 18 A ASN 91 -88.40 -83.04 19 A GLU 7 -115.02 72.29 19 A ALA 9 -167.29 37.85 19 A LYS 19 -106.32 74.93 19 A GLN 51 -100.21 -68.41 19 A PRO 55 -58.27 -78.26 19 A ALA 56 -108.19 46.88 19 A SER 57 -101.95 -61.43 19 A ASN 70 49.32 29.11 19 A GLN 90 -61.72 -145.55 20 A ALA 9 -107.71 49.74 20 A ASP 20 -172.18 83.09 20 A ASP 43 -104.42 44.63 20 A GLN 51 -104.35 -67.77 20 A PRO 55 -57.58 -77.07 20 A ALA 56 -118.34 51.80 20 A ASN 70 45.67 28.46 20 A ASN 76 61.64 71.88 20 A PHE 89 -48.52 171.62 20 A GLN 90 -86.99 -142.47 20 B TRP 303 -145.98 16.54 ERBIN PDZ domain bound to a phage-derived peptide 1 N N 2 N N A GLU 78 A GLU 78 HELX_P A PHE 89 A PHE 89 1 1 12 SIGNALING PROTEIN pdz domain, c-terminal peptide complex, high affnity ligand, SIGNALING PROTEIN A ASP 20 A ASP 20 1 A PRO 21 A PRO 21 0.51 A ASP 20 A ASP 20 2 A PRO 21 A PRO 21 0.42 A ASP 20 A ASP 20 3 A PRO 21 A PRO 21 0.46 A ASP 20 A ASP 20 4 A PRO 21 A PRO 21 0.37 A ASP 20 A ASP 20 5 A PRO 21 A PRO 21 0.47 A ASP 20 A ASP 20 6 A PRO 21 A PRO 21 0.51 A ASP 20 A ASP 20 7 A PRO 21 A PRO 21 0.42 A ASP 20 A ASP 20 8 A PRO 21 A PRO 21 0.24 A ASP 20 A ASP 20 9 A PRO 21 A PRO 21 0.54 A ASP 20 A ASP 20 10 A PRO 21 A PRO 21 0.41 A ASP 20 A ASP 20 11 A PRO 21 A PRO 21 0.65 A ASP 20 A ASP 20 12 A PRO 21 A PRO 21 0.68 A ASP 20 A ASP 20 13 A PRO 21 A PRO 21 0.45 A ASP 20 A ASP 20 14 A PRO 21 A PRO 21 0.50 A ASP 20 A ASP 20 15 A PRO 21 A PRO 21 0.41 A ASP 20 A ASP 20 16 A PRO 21 A PRO 21 0.43 A ASP 20 A ASP 20 17 A PRO 21 A PRO 21 0.62 A ASP 20 A ASP 20 18 A PRO 21 A PRO 21 0.31 A ASP 20 A ASP 20 19 A PRO 21 A PRO 21 0.23 A ASP 20 A ASP 20 20 A PRO 21 A PRO 21 0.19 LAP2_HUMAN UNP 1 1314 Q96RT1 GHELAKQEIRVRVEKDPELGFSISGGVGGRGNPFRPDDDGIFVTRVQPEGPASKLLQPGDKIIQANGYSFINIEHGQAVS LLKTFQNTVELIIVREVSS 1N7T PDB 2 1N7T 1314 1412 1N7T 5 103 Q96RT1 A 1 5 103 301 307 1N7T 301 307 1N7T B 2 1 7 1 cloning artifact GLY 1 1N7T A Q96RT1 UNP 1 1 cloning artifact SER 2 1N7T A Q96RT1 UNP 2 1 cloning artifact HIS 3 1N7T A Q96RT1 UNP 3 1 cloning artifact MET 4 1N7T A Q96RT1 UNP 4 4 3 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A ILE 13 A ILE 13 A GLU 18 A GLU 18 A THR 92 A THR 92 A VAL 98 A VAL 98 A LYS 65 A LYS 65 A ALA 69 A ALA 69 A TYR 72 A TYR 72 A SER 73 A SER 73 A ILE 45 A ILE 45 A PHE 46 A PHE 46 A SER 26 A SER 26 A GLY 29 A GLY 29 B THR 305 B THR 5 B TRP 306 B TRP 6