1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Lu, J. Garcia, J. Dulubova, I. Sudhof, T.C. Rizo, J. 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 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 Biochemistry BICHAW 0033 0006-2960 41 5956 5962 10.1021/bi020050b 11993989 Solution structure of the Vam7p PX domain. 2002 10.2210/pdb1kmd/pdb pdb_00001kmd 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 14418.483 Vacuolar morphogenesis protein VAM7 PX domain, Residues 8-124 1 man polymer Vam7p no no KMSEKLRIKVDDVKINPKYVLYGVSTPNKRLYKRYSEFWKLKTRLERDVGSTIPYDFPEKPGVLDRRWQRRYDDPEMIDE RRIGLERFLNELYNDRFDSRWRDTKIAQDFLQLSKPN KMSEKLRIKVDDVKINPKYVLYGVSTPNKRLYKRYSEFWKLKTRLERDVGSTIPYDFPEKPGVLDRRWQRRYDDPEMIDE RRIGLERFLNELYNDRFDSRWRDTKIAQDFLQLSKPN A 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 baker's yeast Saccharomyces Escherichia Escherichia coli sample 4932 Saccharomyces cerevisiae 511693 Escherichia coli BL21 BL21 PLASMID pGEX-KG database_2 pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Database references Derived calculations 1 0 2002-06-12 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession RCSB Y RCSB 2001-12-14 REL REL The structure was determined using triple-resonance NMR spectroscopy. STRUCTURES WITH THE MINIMAL NOE ENERGY 500 20 3D_15N-separated_NOESY 3D_13C-separated_NOESY 20mM Mes 6.2 1 atm 298 K the structures are based on a total of 1443 restraints, 1193 are NOE-derived distance constraints, 152 dihedral angle restraints, 98 distance restraints from hydrogen bonds. torsion angle dynamics 1 0.5mM Vam7p PX domain U-15N,20mM Mes buffer 90% H2O/10% D2O 0.5mM Vam7p PX domain U-15N, 13C, 20mM Mes buffer 90% H2O/10% D2O 0.5mM Vam7p PX domain U-15N, 20mM Mes Buffer 100% D2O 0.5mM Vam7p PX domain 10%-13C, 20mM Mes buffer 90% H2O/10% D2O DeLaglio, F. et al. processing NMRPipe 1.8 Varian collection VNMR 6.1 Johnson, B. and Blevins R. data analysis NMRView 4.1.2 Brunger, A.T. et al. refinement CNS 1.0 500 Varian INOVA 600 Varian INOVA LYS 8 n 1 LYS 8 A MET 9 n 2 MET 9 A SER 10 n 3 SER 10 A GLU 11 n 4 GLU 11 A LYS 12 n 5 LYS 12 A LEU 13 n 6 LEU 13 A ARG 14 n 7 ARG 14 A ILE 15 n 8 ILE 15 A LYS 16 n 9 LYS 16 A VAL 17 n 10 VAL 17 A ASP 18 n 11 ASP 18 A ASP 19 n 12 ASP 19 A VAL 20 n 13 VAL 20 A LYS 21 n 14 LYS 21 A ILE 22 n 15 ILE 22 A ASN 23 n 16 ASN 23 A PRO 24 n 17 PRO 24 A LYS 25 n 18 LYS 25 A TYR 26 n 19 TYR 26 A VAL 27 n 20 VAL 27 A LEU 28 n 21 LEU 28 A TYR 29 n 22 TYR 29 A GLY 30 n 23 GLY 30 A VAL 31 n 24 VAL 31 A SER 32 n 25 SER 32 A THR 33 n 26 THR 33 A PRO 34 n 27 PRO 34 A ASN 35 n 28 ASN 35 A LYS 36 n 29 LYS 36 A ARG 37 n 30 ARG 37 A LEU 38 n 31 LEU 38 A TYR 39 n 32 TYR 39 A LYS 40 n 33 LYS 40 A ARG 41 n 34 ARG 41 A TYR 42 n 35 TYR 42 A SER 43 n 36 SER 43 A GLU 44 n 37 GLU 44 A PHE 45 n 38 PHE 45 A TRP 46 n 39 TRP 46 A LYS 47 n 40 LYS 47 A LEU 48 n 41 LEU 48 A LYS 49 n 42 LYS 49 A THR 50 n 43 THR 50 A ARG 51 n 44 ARG 51 A LEU 52 n 45 LEU 52 A GLU 53 n 46 GLU 53 A ARG 54 n 47 ARG 54 A ASP 55 n 48 ASP 55 A VAL 56 n 49 VAL 56 A GLY 57 n 50 GLY 57 A SER 58 n 51 SER 58 A THR 59 n 52 THR 59 A ILE 60 n 53 ILE 60 A PRO 61 n 54 PRO 61 A TYR 62 n 55 TYR 62 A ASP 63 n 56 ASP 63 A PHE 64 n 57 PHE 64 A PRO 65 n 58 PRO 65 A GLU 66 n 59 GLU 66 A LYS 67 n 60 LYS 67 A PRO 68 n 61 PRO 68 A GLY 69 n 62 GLY 69 A VAL 70 n 63 VAL 70 A LEU 71 n 64 LEU 71 A ASP 72 n 65 ASP 72 A ARG 73 n 66 ARG 73 A ARG 74 n 67 ARG 74 A TRP 75 n 68 TRP 75 A GLN 76 n 69 GLN 76 A ARG 77 n 70 ARG 77 A ARG 78 n 71 ARG 78 A TYR 79 n 72 TYR 79 A ASP 80 n 73 ASP 80 A ASP 81 n 74 ASP 81 A PRO 82 n 75 PRO 82 A GLU 83 n 76 GLU 83 A MET 84 n 77 MET 84 A ILE 85 n 78 ILE 85 A ASP 86 n 79 ASP 86 A GLU 87 n 80 GLU 87 A ARG 88 n 81 ARG 88 A ARG 89 n 82 ARG 89 A ILE 90 n 83 ILE 90 A GLY 91 n 84 GLY 91 A LEU 92 n 85 LEU 92 A GLU 93 n 86 GLU 93 A ARG 94 n 87 ARG 94 A PHE 95 n 88 PHE 95 A LEU 96 n 89 LEU 96 A ASN 97 n 90 ASN 97 A GLU 98 n 91 GLU 98 A LEU 99 n 92 LEU 99 A TYR 100 n 93 TYR 100 A ASN 101 n 94 ASN 101 A ASP 102 n 95 ASP 102 A ARG 103 n 96 ARG 103 A PHE 104 n 97 PHE 104 A ASP 105 n 98 ASP 105 A SER 106 n 99 SER 106 A ARG 107 n 100 ARG 107 A TRP 108 n 101 TRP 108 A ARG 109 n 102 ARG 109 A ASP 110 n 103 ASP 110 A THR 111 n 104 THR 111 A LYS 112 n 105 LYS 112 A ILE 113 n 106 ILE 113 A ALA 114 n 107 ALA 114 A GLN 115 n 108 GLN 115 A ASP 116 n 109 ASP 116 A PHE 117 n 110 PHE 117 A LEU 118 n 111 LEU 118 A GLN 119 n 112 GLN 119 A LEU 120 n 113 LEU 120 A SER 121 n 114 SER 121 A LYS 122 n 115 LYS 122 A PRO 123 n 116 PRO 123 A ASN 124 n 117 ASN 124 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 LEU 38 A O LEU 31 A N VAL 31 A N VAL 24 A O SER 32 A O SER 25 A N LYS 16 A N LYS 9 A O LEU 38 A O LEU 31 A N VAL 31 A N VAL 24 A O LEU 28 A O LEU 21 A N LYS 21 A N LYS 14 1 A ASP 18 -144.25 27.76 1 A LYS 36 167.70 -176.56 1 A LYS 49 -63.11 -73.96 1 A PRO 61 -88.50 34.05 1 A VAL 70 -81.43 -78.81 1 A LEU 71 -156.32 39.40 1 A ARG 103 -133.33 -62.28 1 A LEU 120 -92.35 38.06 1 A SER 121 -74.23 -168.36 2 A ARG 14 -65.10 98.88 2 A ASP 18 -142.69 25.62 2 A LYS 36 165.52 -179.13 2 A LYS 49 -55.09 -71.48 2 A VAL 70 -77.37 -79.41 2 A ASN 101 -90.48 52.54 2 A ARG 103 -122.84 -67.45 2 A LEU 120 -91.76 38.76 3 A LYS 36 136.16 -178.34 3 A LYS 49 -62.09 -72.80 3 A PRO 61 -88.61 35.11 3 A VAL 70 -103.20 -79.16 3 A LEU 71 -107.11 57.95 3 A LEU 120 -92.30 38.15 3 A SER 121 -105.40 -163.62 4 A LYS 36 166.59 -179.41 4 A LYS 49 -56.17 -70.27 4 A PRO 61 -86.09 34.95 4 A VAL 70 -98.17 -78.98 4 A ARG 73 -141.67 13.44 4 A ASN 101 -95.41 57.43 4 A LEU 120 -92.03 38.59 5 A LYS 36 167.86 -178.37 5 A LYS 49 -55.45 -72.51 5 A PRO 61 -85.52 33.94 5 A VAL 70 -67.37 -79.47 5 A LEU 71 -114.33 70.16 5 A ASN 101 -94.17 52.25 5 A LEU 120 -93.92 40.45 6 A ASP 18 -155.42 26.58 6 A LYS 36 169.18 177.40 6 A LYS 49 -52.54 -72.31 6 A GLU 66 -74.73 -167.16 6 A VAL 70 -124.35 -79.16 6 A LEU 71 -166.70 45.52 6 A ASP 80 -98.90 33.67 6 A ARG 103 -128.64 -50.53 6 A LEU 120 -90.66 37.48 6 A SER 121 57.11 176.40 7 A LYS 36 168.30 -178.30 7 A PRO 61 -87.97 32.58 7 A VAL 70 -124.31 -78.99 7 A ARG 73 -135.86 -43.06 7 A GLN 76 60.19 151.12 7 A ASN 101 -95.34 47.56 7 A ARG 103 -112.52 -78.33 7 A LEU 120 -87.29 39.31 8 A LYS 36 166.62 -178.09 8 A LYS 49 -58.97 -72.69 8 A PRO 61 -87.11 31.05 8 A VAL 70 -60.57 -78.72 8 A LEU 99 -90.04 -60.69 8 A LEU 120 -94.40 41.80 8 A SER 121 -175.04 -166.41 9 A ASP 18 -151.90 26.08 9 A LYS 36 105.99 -169.12 9 A LYS 49 -56.33 -72.39 9 A PRO 61 -87.03 38.13 9 A VAL 70 -91.01 -79.26 9 A LEU 71 -97.41 42.80 9 A LEU 120 -89.44 33.83 10 A ASP 18 -141.24 30.42 10 A LYS 36 167.59 -177.61 10 A LYS 49 -59.25 -70.88 10 A VAL 70 -90.19 -78.21 10 A LEU 71 -93.82 41.62 10 A ARG 74 -158.58 -59.41 10 A ASN 101 -89.71 48.62 10 A LEU 120 -93.35 41.13 11 A LYS 36 169.75 -179.11 11 A LYS 49 -73.39 -71.04 11 A PRO 61 -87.13 42.40 11 A LEU 71 80.15 53.63 11 A ARG 73 -141.00 -55.94 11 A LEU 120 -92.74 38.41 12 A ASP 18 -143.90 24.71 12 A LYS 36 168.73 -178.45 12 A LYS 49 -50.50 -70.80 12 A PRO 61 -84.79 43.41 12 A VAL 70 -100.56 -79.23 12 A ARG 73 -160.89 -43.89 12 A ASN 101 -94.46 45.21 12 A LEU 120 -97.32 37.03 13 A ASP 18 -142.73 23.50 13 A LYS 36 136.76 -179.57 13 A LYS 49 -56.01 -70.92 13 A PRO 61 -86.02 39.33 13 A VAL 70 -75.82 -78.98 13 A ARG 73 -137.92 -44.98 13 A LEU 99 -90.87 -60.43 13 A ARG 103 -120.51 -50.39 13 A LEU 120 -90.16 40.66 13 A SER 121 -70.61 -163.30 14 A LYS 36 168.90 -177.00 14 A LYS 49 -54.43 -72.06 14 A VAL 70 -94.29 -78.93 14 A ARG 73 -157.41 -43.94 14 A ASP 80 -97.11 34.07 14 A LEU 120 -94.23 42.04 15 A LYS 36 167.76 -177.41 15 A LYS 49 -57.44 -75.01 15 A PRO 61 -87.31 32.01 15 A VAL 70 -77.02 -78.84 15 A ARG 73 176.88 -36.59 15 A ARG 103 -127.10 -73.19 15 A LEU 120 -90.31 39.70 16 A LYS 36 99.75 -167.57 16 A LYS 49 -55.73 -72.20 16 A VAL 70 -93.08 -78.90 16 A LEU 71 -103.23 56.89 16 A ARG 73 -133.87 -61.39 16 A LEU 120 -93.72 41.28 17 A LYS 36 137.00 -175.87 17 A LYS 49 -54.06 -71.40 17 A PRO 61 -88.34 34.37 17 A VAL 70 -116.24 -79.29 17 A LEU 71 -144.21 40.03 17 A LEU 99 -91.56 -60.55 17 A LEU 120 -91.87 38.50 18 A LYS 36 133.57 -179.36 18 A LYS 49 -52.42 -72.15 18 A PRO 61 -77.89 47.88 18 A VAL 70 -99.92 -78.87 18 A ASN 101 -95.97 44.31 18 A LEU 120 -92.20 38.89 19 A ASP 18 -140.13 28.47 19 A LYS 36 139.51 178.53 19 A LYS 49 -55.02 -72.73 19 A PRO 61 -87.52 37.80 19 A VAL 70 -86.98 -79.07 19 A LEU 71 -146.85 50.26 19 A ARG 103 -111.06 -77.31 19 A LEU 120 -90.77 37.47 20 A ARG 14 -68.75 98.11 20 A LYS 36 166.66 -178.75 20 A LYS 49 -53.12 -72.03 20 A GLU 66 -77.51 -169.37 20 A VAL 70 -75.07 -79.01 20 A LEU 120 -90.93 36.63 20 A SER 121 57.75 -166.91 SOLUTION STRUCTURE OF THE VAM7P PX DOMAIN 1 N N A ARG 41 A ARG 34 HELX_P A GLY 57 A GLY 50 1 1 17 A ASP 81 A ASP 74 HELX_P A ASN 101 A ASN 94 1 2 21 A SER 106 A SER 99 HELX_P A THR 111 A THR 104 1 3 6 A THR 111 A THR 104 HELX_P A LEU 118 A LEU 111 1 4 8 ENDOCYTOSIS/EXOCYTOSIS PX domain, Vam7p, phosphoinositide binding, ENDOCYTOSIS-EXOCYTOSIS COMPLEX VAM7_YEAST UNP 1 1 P32912 MAANSVGKMSEKLRIKVDDVKINPKYVLYGVSTPNKRLYKRYSEFWKLKTRLERDVGSTIPYDFPEKPGVLDRRWQRRYD DPEMIDERRIGLERFLNELYNDRFDSRWRDTKIAQDFLQLSKPNVSQEKSQQHLETADEVGWDEMIRDIKLDLDKESDGT PSVRGALRARTKLHKLRERLEQDVQKKSLPSTEVTRRAALLRSLLKECDDIGTANIAQDRGRLLGVATSDNSSTTEVQGR TNNDLQQGQMQMVRDQEQELVALHRIIQAQRGLALEMNEELQTQNELLTALEDDVDNTGRRLQIANKKARHFNNSA 8 124 1KMD 8 124 P32912 A 1 1 117 3 3 anti-parallel anti-parallel anti-parallel anti-parallel A LEU 38 A LEU 31 A LYS 40 A LYS 33 A VAL 27 A VAL 20 A SER 32 A SER 25 A LYS 16 A LYS 9 A VAL 17 A VAL 10 A LEU 38 A LEU 31 A LYS 40 A LYS 33 A VAL 27 A VAL 20 A SER 32 A SER 25 A LYS 21 A LYS 14 A ILE 22 A ILE 15