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 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE 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 C3 H8 N2 O2 104.108 n AMINOSERINE 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/pdb1jc8/pdb pdb_00001jc8 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 ATOM OD2 OF ASP 5 IS MISSING DUE TO THE SIDE-CHAIN LINK BETWEEN ASP 5 AND DNP 11 1374.563 DDap: (ACE)IWGDSGKLI(DNP)TTA ANALOGUE OF HIV GP41 1 syn polymer no yes (ACE)IWGDSGKLI(SET)TTA XIWGDSGKLISTTA 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 pdbx_validate_polymer_linkage struct_conn struct_ref_seq_dif repository Initial release Version format compliance Version format compliance Advisory Data collection Database references Derived calculations 1 0 2003-07-01 1 1 2008-04-27 1 2 2011-07-13 1 3 2021-10-27 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model _struct_conn.pdbx_leaving_atom_flag _struct_ref_seq_dif.details 1IM7 contains the parent peptide 1J8N contains a beta3-SER analogue peptide 1J8Z contains a beta3-Cys analogue peptide 1J9V contains the DabD lactam analogue peptide 1JAA contains the DapE lactam analogue peptide. 1JAR contains the DDab lactam analogue peptide RCSB Y RCSB 2001-06-08 REL REL the parent peptide (IWGCSGKLICTTA) occurs naturally in HIV gp41 glycoprotein. sample classical 2D homonuclear NMR techniques were used. Different NOESY experiments with different mixing times from 80ms to 800ms were recorded in order to determine best conditions without spin diffusion. target function 50 20 2D NOESY DQF-COSY TOCSY atmospheric atm 298 K 50 initial random structures were generated usin DYANA software, followed by 500ps restrained minimization, 35ps MD and 750ps conjugated gradient EM using DISCOVER module of MSI software. torsion angles dynamics, molecular dynamics, energy minimization. 1 lowest energy 2mM peptide in 500ul solvent 100% DMSO-D6 Bruker GMBH collection XwinNMR 2.6 Bruker GMBH processing XwinNMR 2.6 Bartels C., 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 ASP 5 n 5 ASP 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 DNP 11 n 11 SET 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 SET 11 AMINOSERINE A SET 11 SER 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 identity operation 0.0000000000 0.0000000000 0.0000000000 1 A OD2 ASP 5 A OD2 ASP 5 1 Y 1 A O SET 11 A O SET 11 1 Y 2 A OD2 ASP 5 A OD2 ASP 5 1 Y 2 A O SET 11 A O SET 11 1 Y 3 A OD2 ASP 5 A OD2 ASP 5 1 Y 3 A O SET 11 A O SET 11 1 Y 4 A OD2 ASP 5 A OD2 ASP 5 1 Y 4 A O SET 11 A O SET 11 1 Y 5 A OD2 ASP 5 A OD2 ASP 5 1 Y 5 A O SET 11 A O SET 11 1 Y 6 A OD2 ASP 5 A OD2 ASP 5 1 Y 6 A O SET 11 A O SET 11 1 Y 7 A OD2 ASP 5 A OD2 ASP 5 1 Y 7 A O SET 11 A O SET 11 1 Y 8 A OD2 ASP 5 A OD2 ASP 5 1 Y 8 A O SET 11 A O SET 11 1 Y 9 A OD2 ASP 5 A OD2 ASP 5 1 Y 9 A O SET 11 A O SET 11 1 Y 10 A OD2 ASP 5 A OD2 ASP 5 1 Y 10 A O SET 11 A O SET 11 1 Y 11 A OD2 ASP 5 A OD2 ASP 5 1 Y 11 A O SET 11 A O SET 11 1 Y 12 A OD2 ASP 5 A OD2 ASP 5 1 Y 12 A O SET 11 A O SET 11 1 Y 13 A OD2 ASP 5 A OD2 ASP 5 1 Y 13 A O SET 11 A O SET 11 1 Y 14 A OD2 ASP 5 A OD2 ASP 5 1 Y 14 A O SET 11 A O SET 11 1 Y 15 A OD2 ASP 5 A OD2 ASP 5 1 Y 15 A O SET 11 A O SET 11 1 Y 16 A OD2 ASP 5 A OD2 ASP 5 1 Y 16 A O SET 11 A O SET 11 1 Y 17 A OD2 ASP 5 A OD2 ASP 5 1 Y 17 A O SET 11 A O SET 11 1 Y 18 A OD2 ASP 5 A OD2 ASP 5 1 Y 18 A O SET 11 A O SET 11 1 Y 19 A OD2 ASP 5 A OD2 ASP 5 1 Y 19 A O SET 11 A O SET 11 1 Y 20 A OD2 ASP 5 A OD2 ASP 5 1 Y 20 A O SET 11 A O SET 11 1 Y 1 A CA SET 11 WRONG HAND 2 A CA SET 11 WRONG HAND 3 A CA SET 11 WRONG HAND 4 A CA SET 11 WRONG HAND 5 A CA SET 11 WRONG HAND 6 A CA SET 11 WRONG HAND 7 A CA SET 11 WRONG HAND 8 A CA SET 11 WRONG HAND 9 A CA SET 11 WRONG HAND 10 A CA SET 11 WRONG HAND 11 A CA SET 11 WRONG HAND 12 A CA SET 11 WRONG HAND 13 A CA SET 11 WRONG HAND 14 A CA SET 11 WRONG HAND 15 A CA SET 11 WRONG HAND 16 A CA SET 11 WRONG HAND 17 A CA SET 11 WRONG HAND 18 A CA SET 11 WRONG HAND 19 A CA SET 11 WRONG HAND 20 A CA SET 11 WRONG HAND 1 A A CG NT ASP SET 5 11 1.34 2 A A CG NT ASP SET 5 11 1.34 3 A A CG NT ASP SET 5 11 1.34 4 A A CG NT ASP SET 5 11 1.34 5 A A CG NT ASP SET 5 11 1.34 6 A A CG NT ASP SET 5 11 1.34 7 A A CG NT ASP SET 5 11 1.34 8 A A CG NT ASP SET 5 11 1.34 9 A A CG NT ASP SET 5 11 1.34 10 A A CG NT ASP SET 5 11 1.34 11 A A CG NT ASP SET 5 11 1.34 12 A A CG NT ASP SET 5 11 1.34 13 A A CG NT ASP SET 5 11 1.34 14 A A CG NT ASP SET 5 11 1.34 15 A A CG NT ASP SET 5 11 1.34 16 A A CG NT ASP SET 5 11 1.34 17 A A CG NT ASP SET 5 11 1.34 18 A A CG NT ASP SET 5 11 1.34 19 A A CG NT ASP SET 5 11 1.34 20 A A CG NT ASP SET 5 11 1.34 1 A A C OXT ALA ALA 14 14 0.142 0.019 1.229 1.371 N 2 A A C OXT ALA ALA 14 14 0.144 0.019 1.229 1.373 N 3 A A C OXT ALA ALA 14 14 0.143 0.019 1.229 1.372 N 4 A A C OXT ALA ALA 14 14 0.143 0.019 1.229 1.372 N 5 A A C OXT ALA ALA 14 14 0.146 0.019 1.229 1.375 N 6 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 7 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 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 0.141 0.019 1.229 1.370 N 10 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 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 0.142 0.019 1.229 1.371 N 13 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 14 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 15 A A C OXT ALA ALA 14 14 0.142 0.019 1.229 1.371 N 16 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 17 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 18 A A C OXT ALA ALA 14 14 0.142 0.019 1.229 1.371 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 0.141 0.019 1.229 1.370 N 1 A LYS 8 -157.92 -71.97 1 A LEU 9 -135.17 -77.57 2 A LYS 8 -159.00 -69.44 2 A LEU 9 -141.88 -74.38 3 A LEU 9 -145.14 -71.43 4 A LYS 8 -160.40 -69.80 4 A LEU 9 -142.26 -73.34 5 A LYS 8 -161.12 -73.11 5 A LEU 9 -138.85 -73.04 6 A LYS 8 -159.62 -75.78 6 A LEU 9 -133.56 -73.05 7 A LYS 8 -159.92 -75.01 7 A LEU 9 -133.92 -71.93 8 A LEU 9 -137.37 -69.08 9 A LYS 8 -160.16 -76.17 9 A LEU 9 -134.75 -72.79 10 A LYS 8 -161.33 -70.87 10 A LEU 9 -140.83 -72.86 11 A TRP 3 -90.39 -64.48 11 A LYS 8 -161.44 -70.89 11 A LEU 9 -138.62 -74.32 12 A LYS 8 -158.79 -75.12 12 A LEU 9 -134.75 -72.92 13 A LEU 9 -143.86 -77.06 14 A LYS 8 -145.52 -65.69 14 A LEU 9 -152.60 -69.62 14 A THR 13 -106.34 79.98 15 A LYS 8 -159.60 -70.00 15 A LEU 9 -139.79 -73.76 16 A LYS 8 -159.90 -68.76 16 A LEU 9 -141.99 -73.95 17 A LYS 8 -158.90 -63.29 17 A LEU 9 -142.32 -74.02 18 A LYS 8 -159.69 -67.12 18 A LEU 9 -144.82 -59.70 19 A LYS 8 -160.45 -71.90 19 A LEU 9 -148.02 -69.46 20 A LYS 8 -161.22 -69.55 20 A LEU 9 -144.23 -67.96 Solution structure of lactam analogue (DDap) of gp41 600-612 loop of HIV 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 1.347 both A ILE 10 A C ILE 10 1_555 A SET 11 A N SET 11 1_555 covale 1.350 one A SET 11 A CB SET 11 1_555 A THR 12 A N THR 12 1_555 VIRAL PROTEIN lactam bond, cyclic peptide, HIV gp41, peptidomimetics., Viral protein ENV_HV1BN UNP 1 591 P12488 IWGCSGKLICTTA 591 603 1JC8 2 14 P12488 A 1 2 14 1 acetylation ACE 1 1JC8 A P12488 UNP 1 1 CYS engineered mutation ASP 5 1JC8 A P12488 UNP 594 5 1 CYS engineered mutation SET 11 1JC8 A P12488 UNP 600 11