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 C4 H10 N2 O2 118.134 n 2,4-DIAMINOBUTYRIC 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/pdb1jar/pdb pdb_00001jar 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 1388.589 DDab: (ACE)IWGDSGKLI(DAB)TTA ANALOGUE OF HIV GP41 1 man polymer no yes (ACE)IWGDSGKLI(DAB)TTA XIWGDSGKLIATTA 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 struct_ref_seq_dif 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 2021-10-27 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_ref_seq_dif.details The 1IM7 entry contains the parent peptide. The 1J8N entry contains the beta3-SER containg analogue (HSER) The 1J8Z entry contains the beta3-Cys containg analogue peptide (HCYS) The 1J9V entry contains the lactam analogue DabD The 1JAA entry contains the lactam analogue DapE RCSB Y RCSB 2001-05-31 REL REL The parent peptide (IWGCSGKLICTTA) occurs naturaly in HIV gp41 glycoprotein. sample the structure was calculated using standard 2D homonuclear techniques. Different NOSY experiments were recorded in order to determined the best conditions avoiding spin diffusion target function 50 49 2D NOESY DQF-COSY TOCSY none ambient 298 K 50 initial radom structure are generated using DYANA software.followed by 500 ps restrained minimization. Followed by 750 ps conjugated gradient EM using the DISCOVER module of MSI software. torsion angle dynalmics, molecular dynanmics, energy minimization 1 lowest energy 4mM peptide in 500ul DMSO-D6 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 (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 Molecular Simulation Inc. 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 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 identity operation 0.0000000000 0.0000000000 0.0000000000 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 0.143 0.019 1.229 1.372 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 0.146 0.019 1.229 1.375 N 5 A A C OXT ALA ALA 14 14 0.145 0.019 1.229 1.374 N 6 A A C OXT ALA ALA 14 14 0.145 0.019 1.229 1.374 N 7 A A C OXT ALA ALA 14 14 0.146 0.019 1.229 1.375 N 8 A A C OXT ALA ALA 14 14 0.145 0.019 1.229 1.374 N 9 A A C OXT ALA ALA 14 14 0.147 0.019 1.229 1.376 N 10 A A C OXT ALA ALA 14 14 0.144 0.019 1.229 1.373 N 11 A A C OXT ALA ALA 14 14 0.143 0.019 1.229 1.372 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 0.142 0.019 1.229 1.371 N 14 A A C OXT ALA ALA 14 14 0.144 0.019 1.229 1.373 N 15 A A C OXT ALA ALA 14 14 0.144 0.019 1.229 1.373 N 16 A A C OXT ALA ALA 14 14 0.143 0.019 1.229 1.372 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 0.143 0.019 1.229 1.372 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 0.145 0.019 1.229 1.374 N 22 A A C OXT ALA ALA 14 14 0.144 0.019 1.229 1.373 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 0.141 0.019 1.229 1.370 N 25 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 26 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 27 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 28 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 29 A A C OXT ALA ALA 14 14 0.142 0.019 1.229 1.371 N 30 A A C OXT ALA ALA 14 14 0.142 0.019 1.229 1.371 N 31 A A C OXT ALA ALA 14 14 0.142 0.019 1.229 1.371 N 32 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 33 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 34 A A C OXT ALA ALA 14 14 0.142 0.019 1.229 1.371 N 35 A A C OXT ALA ALA 14 14 0.141 0.019 1.229 1.370 N 36 A A C OXT ALA ALA 14 14 0.146 0.019 1.229 1.375 N 37 A A C OXT ALA ALA 14 14 0.145 0.019 1.229 1.374 N 38 A A C OXT ALA ALA 14 14 0.143 0.019 1.229 1.372 N 39 A A C OXT ALA ALA 14 14 0.143 0.019 1.229 1.372 N 40 A A C OXT ALA ALA 14 14 0.144 0.019 1.229 1.373 N 41 A A C OXT ALA ALA 14 14 0.143 0.019 1.229 1.372 N 42 A A C OXT ALA ALA 14 14 0.144 0.019 1.229 1.373 N 43 A A C OXT ALA ALA 14 14 0.144 0.019 1.229 1.373 N 44 A A C OXT ALA ALA 14 14 0.146 0.019 1.229 1.375 N 45 A A C OXT ALA ALA 14 14 0.145 0.019 1.229 1.374 N 46 A A C OXT ALA ALA 14 14 0.145 0.019 1.229 1.374 N 47 A A C OXT ALA ALA 14 14 0.147 0.019 1.229 1.376 N 48 A A C OXT ALA ALA 14 14 0.143 0.019 1.229 1.372 N 49 A A C OXT ALA ALA 14 14 0.144 0.019 1.229 1.373 N 1 A THR 12 -72.69 -85.21 2 A THR 13 -124.50 -73.70 7 A THR 13 -91.55 -69.90 12 A ILE 10 -158.28 82.02 15 A TRP 3 -112.32 68.49 19 A ILE 10 -154.11 83.68 20 A SER 6 -158.93 85.72 20 A ILE 10 -152.46 86.40 22 A TRP 3 -114.01 50.80 22 A ILE 10 -156.40 86.09 23 A SER 6 -156.24 85.84 30 A ILE 10 -163.59 70.52 31 A ILE 10 -163.23 70.19 32 A ILE 10 -161.66 69.93 33 A ILE 10 -160.61 68.88 34 A ILE 10 -164.74 70.57 35 A ILE 10 -162.41 70.78 36 A ILE 10 -160.03 67.77 37 A ILE 10 -161.85 67.93 38 A ILE 10 -154.40 72.26 39 A ILE 10 -160.40 81.67 40 A ILE 10 -161.34 80.08 41 A ILE 10 -158.12 74.14 42 A ILE 10 -163.07 68.41 43 A ILE 10 -151.54 75.33 43 A DAB 11 -104.22 61.24 45 A ILE 10 -145.05 55.61 46 A ILE 10 -161.25 73.12 47 A ILE 10 -159.09 75.44 47 A DAB 11 -105.06 52.81 48 A ILE 10 -151.42 77.99 48 A DAB 11 -115.52 69.67 49 A ILE 10 -162.07 77.18 49 A DAB 11 -112.14 71.59 Solution structure of lactam analogue (DDab)of HIV gp41 600-612 loop. 1 N N covale 1.341 both A ACE 1 A C ACE 1 1_555 A ILE 2 A N ILE 2 1_555 covale 1.342 none A ASP 5 A CG ASP 5 1_555 A DAB 11 A ND DAB 11 1_555 covale 1.353 both A ILE 10 A C ILE 10 1_555 A DAB 11 A N DAB 11 1_555 covale 1.357 both A DAB 11 A C DAB 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 1JAR 2 14 P12488 A 1 2 14 1 acetylation ACE 1 1JAR A P12488 UNP 1 1 CYS engineered mutation ASP 5 1JAR A P12488 UNP 594 5 1 CYS engineered mutation DAB 11 1JAR A P12488 UNP 600 11