1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Phan Chan Du, A. Limal, D. Semetey, V. Dali, H. Jolivet, M. Desgranges, C. Cung, M.T. Briand, J.P. Petit, M.C. Muller, S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 C2 H4 O 44.053 ACETYL GROUP non-polymer C3 H7 N O2 89.093 y ALANINE L-peptide linking C4 H10 N2 O2 118.134 n 2,4-DIAMINOBUTYRIC ACID 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 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 UK J.Mol.Biol. JMOBAK 0070 0022-2836 323 503 521 10.1016/S0022-2836(02)00701-5 12381305 Structural and immunological characterisation of heteroclitic peptide analogues corresponding to the 600-612 region of the HIV envelope gp41 glycoprotein. 2002 10.2210/pdb1jdk/pdb pdb_00001jdk 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 1402.615 ACETYL GROUP 1 syn polymer no yes (ACE)IWGESGKLI(DAB)TTA XIWGESGKLIATTA A polypeptide(L) 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 repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2003-07-01 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 1IM7 contains the parent peptide AcIWGCSGKLICTTA. 1J8N contains a beta3-Ser containing analogue peptide (HSER) 1J8Z contains a beta3-Cys containing analogue peptide (HCYS) 1J9V contains the lactam analogue DabD 1JAR contains the lactam analogue peptide DDab 1JC8 contains the lactam analogue peptide DDap 1JAA contains the lactam analogue peptide DapE 1JCP contains the lactam analogue peptide EDap 1JD8 contains the lactam analogue peptide DapD RCSB Y RCSB 2001-06-14 REL REL the parent peptide IWGCSGKLICTTA occurs naturally in HIV gp41 glycoprotein sample Typical 2D ho;onuclear techniques were applied. Different NOESY experiment with different mixing times (from 80ms to 800ms) were recorded in order to determine the best conditions without spin diffusion. target function 50 25 2D NOESY DQF-COSY TOCSY atmospheric atm 298 K 50 initial random strucutre were generated using DYANA software, followed by 500 steps energy minimization. Then using DISCOVER 3 35 ps MD in vacuo at 300K, 200 steps energy minimization under NMR restraints and 750 steps conjugate gradient EM. torsion angle dynamics, energy minimization, molecular dynamics 1 lowest energy 3mMpeptide in 500ul solvent 100% DMSO-D6 Bruker GMBH collection XwinNMR 2.6 Bruker GMBH processing XwinNMR 2.6 Bartels C., Xia T., Billeter M., Guentert P and Wuethrich K. (1995) J. Biomol.NMR, 5, 1-10 data analysis XEASY 1.2 Guentert P., Mumenthaler C. and Wuethrich K. (1997) J.Mol.Biol., 273,283-298 refinement DYANA 1.5 MSI, San Diego refinement Discover 3 400 Bruker AVANCE 600 Bruker AVANCE ACE 1 n 1 ACE 1 A ILE 2 n 2 ILE 2 A TRP 3 n 3 TRP 3 A GLY 4 n 4 GLY 4 A GLU 5 n 5 GLU 5 A SER 6 n 6 SER 6 A GLY 7 n 7 GLY 7 A LYS 8 n 8 LYS 8 A LEU 9 n 9 LEU 9 A ILE 10 n 10 ILE 10 A DAB 11 n 11 DAB 11 A THR 12 n 12 THR 12 A THR 13 n 13 THR 13 A ALA 14 n 14 ALA 14 A author_defined_assembly 1 monomeric A DAB 11 2,4-DIAMINOBUTYRIC ACID A DAB 11 ALA 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 OE2 GLU 5 A OE2 GLU 5 1 Y 2 A OE2 GLU 5 A OE2 GLU 5 1 Y 3 A OE2 GLU 5 A OE2 GLU 5 1 Y 4 A OE2 GLU 5 A OE2 GLU 5 1 Y 5 A OE2 GLU 5 A OE2 GLU 5 1 Y 6 A OE2 GLU 5 A OE2 GLU 5 1 Y 7 A OE2 GLU 5 A OE2 GLU 5 1 Y 8 A OE2 GLU 5 A OE2 GLU 5 1 Y 9 A OE2 GLU 5 A OE2 GLU 5 1 Y 10 A OE2 GLU 5 A OE2 GLU 5 1 Y 11 A OE2 GLU 5 A OE2 GLU 5 1 Y 12 A OE2 GLU 5 A OE2 GLU 5 1 Y 13 A OE2 GLU 5 A OE2 GLU 5 1 Y 14 A OE2 GLU 5 A OE2 GLU 5 1 Y 15 A OE2 GLU 5 A OE2 GLU 5 1 Y 16 A OE2 GLU 5 A OE2 GLU 5 1 Y 17 A OE2 GLU 5 A OE2 GLU 5 1 Y 18 A OE2 GLU 5 A OE2 GLU 5 1 Y 19 A OE2 GLU 5 A OE2 GLU 5 1 Y 20 A OE2 GLU 5 A OE2 GLU 5 1 Y 21 A OE2 GLU 5 A OE2 GLU 5 1 Y 22 A OE2 GLU 5 A OE2 GLU 5 1 Y 23 A OE2 GLU 5 A OE2 GLU 5 1 Y 24 A OE2 GLU 5 A OE2 GLU 5 1 Y 25 A OE2 GLU 5 A OE2 GLU 5 1 Y 1 A A CD ND GLU DAB 5 11 1.34 2 A A CD ND GLU DAB 5 11 1.34 3 A A CD ND GLU DAB 5 11 1.34 4 A A CD ND GLU DAB 5 11 1.35 5 A A CD ND GLU DAB 5 11 1.34 6 A A CD ND GLU DAB 5 11 1.34 7 A A CD ND GLU DAB 5 11 1.34 8 A A CD ND GLU DAB 5 11 1.34 9 A A CD ND GLU DAB 5 11 1.34 10 A A CD ND GLU DAB 5 11 1.34 11 A A CD ND GLU DAB 5 11 1.34 12 A A CD ND GLU DAB 5 11 1.34 13 A A CD ND GLU DAB 5 11 1.34 14 A A CD ND GLU DAB 5 11 1.34 15 A A CD ND GLU DAB 5 11 1.34 16 A A CD ND GLU DAB 5 11 1.35 17 A A CD ND GLU DAB 5 11 1.35 18 A A CD ND GLU DAB 5 11 1.34 19 A A CD ND GLU DAB 5 11 1.34 20 A A CD ND GLU DAB 5 11 1.35 21 A A CD ND GLU DAB 5 11 1.34 22 A A CD ND GLU DAB 5 11 1.34 23 A A CD ND GLU DAB 5 11 1.34 24 A A CD ND GLU DAB 5 11 1.34 25 A A CD ND GLU DAB 5 11 1.34 1 A A C OXT ALA ALA 14 14 0.143 0.019 1.229 1.372 N 2 A A C OXT ALA ALA 14 14 0.146 0.019 1.229 1.375 N 3 A A C OXT ALA ALA 14 14 0.144 0.019 1.229 1.373 N 4 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 5 A A C OXT ALA ALA 14 14 0.144 0.019 1.229 1.373 N 6 A A C OXT ALA ALA 14 14 0.146 0.019 1.229 1.375 N 7 A A C OXT ALA ALA 14 14 0.145 0.019 1.229 1.374 N 8 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 9 A A C OXT ALA ALA 14 14 0.144 0.019 1.229 1.373 N 10 A A C OXT ALA ALA 14 14 0.142 0.019 1.229 1.371 N 11 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 12 A A C OXT ALA ALA 14 14 0.144 0.019 1.229 1.373 N 13 A A C OXT ALA ALA 14 14 0.145 0.019 1.229 1.374 N 14 A A C OXT ALA ALA 14 14 0.142 0.019 1.229 1.371 N 15 A A C OXT ALA ALA 14 14 0.147 0.019 1.229 1.376 N 16 A A C OXT ALA ALA 14 14 0.144 0.019 1.229 1.373 N 17 A A C OXT ALA ALA 14 14 0.144 0.019 1.229 1.373 N 18 A A C OXT ALA ALA 14 14 0.143 0.019 1.229 1.372 N 19 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 20 A A C OXT ALA ALA 14 14 0.146 0.019 1.229 1.375 N 21 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 22 A A C OXT ALA ALA 14 14 0.145 0.019 1.229 1.374 N 23 A A C OXT ALA ALA 14 14 0.144 0.019 1.229 1.373 N 24 A A C OXT ALA ALA 14 14 0.144 0.019 1.229 1.373 N 25 A A C OXT ALA ALA 14 14 0.145 0.019 1.229 1.374 N 1 A SER 6 -136.00 -109.87 1 A LEU 9 -147.49 -71.50 2 A THR 12 -163.52 115.63 3 A LYS 8 -153.29 -58.66 3 A LEU 9 -69.47 -72.09 3 A DAB 11 -169.43 101.45 4 A THR 12 -124.75 -88.23 5 A SER 6 -138.44 -115.97 5 A LYS 8 -129.15 -83.52 5 A LEU 9 -97.36 -71.49 5 A THR 12 -80.67 -92.05 6 A LEU 9 -140.15 -58.92 7 A SER 6 -86.19 -116.74 7 A LYS 8 -110.64 -163.60 8 A LYS 8 -91.36 -68.88 8 A LEU 9 -145.99 -66.08 9 A LEU 9 -121.78 -83.99 9 A THR 12 -141.39 -72.17 10 A GLU 5 -133.74 -33.89 11 A SER 6 -150.06 -138.21 11 A LYS 8 -143.84 -68.29 11 A LEU 9 -115.39 -71.43 12 A LEU 9 -149.58 -59.84 13 A LYS 8 -97.71 -70.81 13 A LEU 9 -141.67 -68.59 14 A SER 6 -136.69 -126.32 15 A THR 12 -124.53 -74.52 15 A THR 13 -133.25 -61.55 16 A SER 6 -127.02 -129.05 16 A LYS 8 -143.90 -76.64 16 A LEU 9 -125.89 -80.07 17 A LEU 9 -78.29 -75.96 18 A THR 13 -91.37 -63.36 19 A GLU 5 -103.90 59.52 19 A SER 6 -179.10 -97.02 19 A LYS 8 -147.83 -57.97 19 A LEU 9 -128.55 -72.89 20 A LEU 9 -126.47 -98.22 20 A THR 12 -126.17 -72.63 21 A LYS 8 -98.46 -80.91 21 A LEU 9 -118.64 -72.63 22 A GLU 5 -118.51 72.31 22 A SER 6 -163.14 87.65 23 A SER 6 -141.23 -121.47 25 A SER 6 -130.29 -113.01 solution structure of lactam analogue (EDap) of HIV gp41 600-612 loop. 1 N N covale 1.340 both A ACE 1 A C ACE 1 1_555 A ILE 2 A N ILE 2 1_555 covale 1.352 both A ILE 10 A C ILE 10 1_555 A DAB 11 A N DAB 11 1_555 covale 1.359 both A DAB 11 A C DAB 11 1_555 A THR 12 A N THR 12 1_555 VIRAL PROTEIN cyclic peptide, peptidomimetics, HIV, gp41, lactam bond, Viral protein 1JDK PDB 1 1JDK 1 14 1JDK 1 14 1JDK A 1 1 14