1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Schibli, D.J. Montelaro, R.C. Vogel, H.J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C3 H7 N O2 89.093 y ALANINE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE 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 H2 N 16.023 AMINO GROUP non-polymer C9 H11 N O2 165.189 y PHENYLALANINE 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 US Biochemistry BICHAW 0033 0006-2960 40 9570 9578 10.1021/bi010640u 11583156 The membrane-proximal tryptophan-rich region of the HIV glycoprotein, gp41, forms a well-defined helix in dodecylphosphocholine micelles. 2001 10.2210/pdb1jau/pdb pdb_00001jau 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 2569.979 TRANSMEMBRANE GLYCOPROTEIN (GP41) residues 665-683 1 syn polymer no yes KWASLWNWFNITNWLWYIK(NH2) KWASLWNWFNITNWLWYIKX A polypeptide(L) n n n n n n n n n n n n n n n n n n n n database_2 pdbx_nmr_software pdbx_nmr_spectrometer pdbx_struct_assembly pdbx_struct_oper_list struct_conn struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2001-10-17 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model _struct_conn.pdbx_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Minimized Average Structure for this deposition RCSB Y RCSB 2001-05-31 REL REL This peptide was chemically synthesized. The sequence of the peptide is naturally found in Human Immunodeficiency Virus (HIV). sample This structure was determined using standard 2D homonuclear techniques. structures with the lowest energy 200 40 2D NOESY 2D TOCSY DQF-COSY 2D NOESY 2D TOCSY 200 mM DPC-d38 3.51 ambient 310 K Structures were initially generated using CNS. Ambiguous and unassigned noe constraints were then used in conjuction with matrix relaxation analysis using the program ARIA. distance geometry, simulated annealing, molecular dynamics, matrix relaxation 1.6 mM synthetic gp41 peptide, 200 mM perdeuterated dodecylphosphocholine 90% H2O/10% D2O 1.6 mM synthetic gp41 peptide, 200 mM perdeuterated dodecylphosphocholine 100% D2O Bruker collection XwinNMR 2.6 F.Delaglio, S.Grzesiek, G.Vuister, G.Zhu, J.Pfeifer, A.Bax processing NMRPipe 1.8 B.Johnson, R.A.Blevins data analysis NMRView 4.1.3 A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warren structure solution CNS 1.0 M.Nilges, J.Linge, S.O'Donoghue iterative matrix relaxation ARIA 1.0 A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warren refinement CNS 1.0 500 Bruker AVANCE 800 Varian INOVA LYS 1 n 1 LYS 1 A TRP 2 n 2 TRP 2 A ALA 3 n 3 ALA 3 A SER 4 n 4 SER 4 A LEU 5 n 5 LEU 5 A TRP 6 n 6 TRP 6 A ASN 7 n 7 ASN 7 A TRP 8 n 8 TRP 8 A PHE 9 n 9 PHE 9 A ASN 10 n 10 ASN 10 A ILE 11 n 11 ILE 11 A THR 12 n 12 THR 12 A ASN 13 n 13 ASN 13 A TRP 14 n 14 TRP 14 A LEU 15 n 15 LEU 15 A TRP 16 n 16 TRP 16 A TYR 17 n 17 TYR 17 A ILE 18 n 18 ILE 18 A LYS 19 n 19 LYS 19 A LYS 19 n 20 NH2 20 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 -27.22 1.60 122.70 95.48 A A A O C N LYS LYS NH2 19 19 20 Y 3 -10.06 1.60 122.70 112.64 A A A O C N LYS LYS NH2 19 19 20 Y 4 -38.44 1.60 122.70 84.26 A A A O C N LYS LYS NH2 19 19 20 Y 5 -42.36 1.60 122.70 80.34 A A A O C N LYS LYS NH2 19 19 20 Y 6 -22.93 1.60 122.70 99.77 A A A O C N LYS LYS NH2 19 19 20 Y 7 -11.84 1.60 122.70 110.86 A A A O C N LYS LYS NH2 19 19 20 Y 9 -56.58 1.60 122.70 66.12 A A A O C N LYS LYS NH2 19 19 20 Y 10 -38.24 1.60 122.70 84.46 A A A O C N LYS LYS NH2 19 19 20 Y 11 -20.23 1.60 122.70 102.47 A A A O C N LYS LYS NH2 19 19 20 Y 12 -13.54 1.60 122.70 109.16 A A A O C N LYS LYS NH2 19 19 20 Y 13 -20.27 1.60 122.70 102.43 A A A O C N LYS LYS NH2 19 19 20 Y 15 -46.75 1.60 122.70 75.95 A A A O C N LYS LYS NH2 19 19 20 Y 16 -47.04 1.60 122.70 75.66 A A A O C N LYS LYS NH2 19 19 20 Y 19 -33.08 1.60 122.70 89.62 A A A O C N LYS LYS NH2 19 19 20 Y 20 -11.75 1.60 122.70 110.95 A A A O C N LYS LYS NH2 19 19 20 Y 21 -52.26 1.60 122.70 70.44 A A A O C N LYS LYS NH2 19 19 20 Y 23 -9.73 1.60 122.70 112.97 A A A O C N LYS LYS NH2 19 19 20 Y 25 -28.81 1.60 122.70 93.89 A A A O C N LYS LYS NH2 19 19 20 Y 27 -11.42 1.60 122.70 111.28 A A A O C N LYS LYS NH2 19 19 20 Y 30 -9.71 1.60 122.70 112.99 A A A O C N LYS LYS NH2 19 19 20 Y 33 -29.41 1.60 122.70 93.29 A A A O C N LYS LYS NH2 19 19 20 Y 34 -61.35 1.60 122.70 61.35 A A A O C N LYS LYS NH2 19 19 20 Y 35 -47.13 1.60 122.70 75.57 A A A O C N LYS LYS NH2 19 19 20 Y 39 -27.67 1.60 122.70 95.03 A A A O C N LYS LYS NH2 19 19 20 Y 1 A ALA 3 -78.02 30.38 1 A LEU 5 -140.42 -26.28 2 A ALA 3 -79.74 29.42 2 A THR 12 -68.33 1.66 3 A THR 12 -68.75 0.56 4 A ALA 3 -79.15 27.58 5 A THR 12 -66.30 1.19 7 A ALA 3 -75.59 25.28 7 A THR 12 -68.58 2.11 7 A ILE 18 -76.51 -70.60 8 A ALA 3 -77.79 24.97 9 A ALA 3 -78.20 23.27 10 A ALA 3 -73.79 22.13 11 A ALA 3 -75.84 27.94 11 A THR 12 -67.49 1.83 12 A ALA 3 -69.83 5.62 13 A THR 12 -68.17 0.70 14 A ALA 3 -76.55 21.21 15 A ALA 3 -75.37 27.72 15 A THR 12 -67.67 0.61 17 A THR 12 -67.35 1.82 19 A TRP 2 -153.52 26.55 20 A ALA 3 -77.27 21.18 21 A ALA 3 -77.48 23.03 22 A ALA 3 -77.43 24.78 23 A ALA 3 -78.68 22.47 24 A ALA 3 -78.40 29.14 24 A SER 4 -141.32 53.62 24 A LEU 5 -144.91 -16.47 26 A SER 4 -98.30 34.39 26 A THR 12 -67.18 0.63 27 A ALA 3 -77.59 23.97 28 A THR 12 -68.64 3.72 29 A ALA 3 -78.59 25.32 30 A ALA 3 -75.39 27.72 30 A THR 12 -69.43 5.08 31 A ALA 3 -78.83 30.76 31 A LEU 5 -140.93 -3.25 31 A THR 12 -67.11 2.16 32 A ALA 3 -78.56 24.80 33 A ALA 3 -78.89 31.10 34 A ALA 3 -69.65 11.92 34 A ILE 18 -82.87 -74.70 35 A ALA 3 -77.94 30.26 37 A SER 4 -99.56 30.71 38 A ALA 3 -79.17 30.52 38 A THR 12 -68.20 0.11 38 A ILE 18 -96.07 -74.92 40 A TRP 2 -69.64 5.01 40 A ALA 3 -68.05 5.41 NMR Solution Structure of the Trp-Rich Peptide of HIV gp41 Bound to DPC Micelles 1 N N A LEU 5 A LEU 5 HELX_P A ASN 10 A ASN 10 1 1 6 A ASN 10 A ASN 10 HELX_P A LYS 19 A LYS 19 1 2 10 covale 1.328 both A LYS 19 A C LYS 19 1_555 A NH2 20 A N NH2 20 1_555 covale 1.908 one A LYS 19 A O LYS 19 1_555 A NH2 20 A N NH2 20 1_555 VIRAL PROTEIN amphipathic alpha helix, Viral protein ENV_HV1H3 UNP 1 665 P04624 KWASLWNWFNITNWLWYIK 665 683 1JAU 1 19 P04624 A 1 1 19 BINDING SITE FOR RESIDUE NH2 A 20 A NH2 20 Software 2 A TRP 16 A TRP 16 2 1_555 A LYS 19 A LYS 19 2 1_555