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 C3 H7 N O2 S 121.158 y CYSTEINE 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 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/pdb1jcp/pdb pdb_00001jcp 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 OE2 OF GLU 5 IS MISSING DUE TO THE SIDE-CHAIN LINK BETWEEN GLU 5 AND DNP 11 1388.589 Edap : ACE-Ile-Trp-Glu-Ser-Gly-Lys-Leu-Ile-Dap-Thr-Thr-Ala ANALOGUE OF HIV GP41 1 man polymer no yes (ACE)IWGESGKLI(SET)TTA XIWGESGKLISTTA 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 struct_site 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 _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id 1IM7 contains the parent peptide 1J8N contains a beta3-Ser analogue 1J8Z contains a beta3 Cys analogue 1J9V a lactam analogue DabD 1JAR : DDab a lactam analogue 1JC8 contains a lactam analogue DDap 1JAA contains a lactam analogue DapE RCSB Y RCSB 2001-06-11 REL REL The parent peptide (IWGCSGKLICTTA) occurs naturally in HIV gp41. 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 the best conditions without spin diffusion. target function 50 20 DQF-COSY 2D NOESY TOCSY atmospheric atm 298 K 50 initial structures were generated using DYANA software, followed by 500 ps restrained energy minimization. Then using DISCOVER 35 ps MD, 750ps conjugated gradient EM . torsion angle dynamics, molecular dynamics, energy minimization. 1 lowest energy 4mM 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, 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 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 OE2 GLU 5 A OE2 GLU 5 1 Y 1 A O SET 11 A O SET 11 1 Y 2 A OE2 GLU 5 A OE2 GLU 5 1 Y 2 A O SET 11 A O SET 11 1 Y 3 A OE2 GLU 5 A OE2 GLU 5 1 Y 3 A O SET 11 A O SET 11 1 Y 4 A OE2 GLU 5 A OE2 GLU 5 1 Y 4 A O SET 11 A O SET 11 1 Y 5 A OE2 GLU 5 A OE2 GLU 5 1 Y 5 A O SET 11 A O SET 11 1 Y 6 A OE2 GLU 5 A OE2 GLU 5 1 Y 6 A O SET 11 A O SET 11 1 Y 7 A OE2 GLU 5 A OE2 GLU 5 1 Y 7 A O SET 11 A O SET 11 1 Y 8 A OE2 GLU 5 A OE2 GLU 5 1 Y 8 A O SET 11 A O SET 11 1 Y 9 A OE2 GLU 5 A OE2 GLU 5 1 Y 9 A O SET 11 A O SET 11 1 Y 10 A OE2 GLU 5 A OE2 GLU 5 1 Y 10 A O SET 11 A O SET 11 1 Y 11 A OE2 GLU 5 A OE2 GLU 5 1 Y 11 A O SET 11 A O SET 11 1 Y 12 A OE2 GLU 5 A OE2 GLU 5 1 Y 12 A O SET 11 A O SET 11 1 Y 13 A OE2 GLU 5 A OE2 GLU 5 1 Y 13 A O SET 11 A O SET 11 1 Y 14 A OE2 GLU 5 A OE2 GLU 5 1 Y 14 A O SET 11 A O SET 11 1 Y 15 A OE2 GLU 5 A OE2 GLU 5 1 Y 15 A O SET 11 A O SET 11 1 Y 16 A OE2 GLU 5 A OE2 GLU 5 1 Y 16 A O SET 11 A O SET 11 1 Y 17 A OE2 GLU 5 A OE2 GLU 5 1 Y 17 A O SET 11 A O SET 11 1 Y 18 A OE2 GLU 5 A OE2 GLU 5 1 Y 18 A O SET 11 A O SET 11 1 Y 19 A OE2 GLU 5 A OE2 GLU 5 1 Y 19 A O SET 11 A O SET 11 1 Y 20 A OE2 GLU 5 A OE2 GLU 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 CD NT GLU SET 5 11 1.34 2 A A CD NT GLU SET 5 11 1.34 3 A A CD NT GLU SET 5 11 1.34 4 A A CD NT GLU SET 5 11 1.34 5 A A CD NT GLU SET 5 11 1.34 6 A A CD NT GLU SET 5 11 1.34 7 A A CD NT GLU SET 5 11 1.34 8 A A CD NT GLU SET 5 11 1.34 9 A A CD NT GLU SET 5 11 1.34 10 A A CD NT GLU SET 5 11 1.34 11 A A CD NT GLU SET 5 11 1.35 12 A A CD NT GLU SET 5 11 1.34 13 A A CD NT GLU SET 5 11 1.35 14 A A CD NT GLU SET 5 11 1.35 15 A A CD NT GLU SET 5 11 1.34 16 A A CD NT GLU SET 5 11 1.34 17 A A CD NT GLU SET 5 11 1.34 18 A A CD NT GLU SET 5 11 1.34 19 A A CD NT GLU SET 5 11 1.34 20 A A CD NT GLU SET 5 11 1.34 1 A A C OXT ALA ALA 14 14 0.140 0.019 1.229 1.369 N 2 A A C OXT ALA ALA 14 14 0.142 0.019 1.229 1.371 N 3 A A C OXT ALA ALA 14 14 0.142 0.019 1.229 1.371 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 0.145 0.019 1.229 1.374 N 6 A A C OXT ALA ALA 14 14 0.144 0.019 1.229 1.373 N 7 A A C OXT ALA ALA 14 14 0.142 0.019 1.229 1.371 N 8 A A C OXT ALA ALA 14 14 0.147 0.019 1.229 1.376 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 0.146 0.019 1.229 1.375 N 11 A A C OXT ALA ALA 14 14 0.145 0.019 1.229 1.374 N 12 A A C OXT ALA ALA 14 14 0.145 0.019 1.229 1.374 N 13 A A C OXT ALA ALA 14 14 0.144 0.019 1.229 1.373 N 14 A A C OXT ALA ALA 14 14 0.146 0.019 1.229 1.375 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 0.145 0.019 1.229 1.374 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 0.144 0.019 1.229 1.373 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 0.141 0.019 1.229 1.370 N 2 A GLU 5 -110.89 75.41 3 A SER 6 -163.06 88.80 4 A SER 6 -163.13 88.93 5 A SER 6 -160.48 94.96 6 A SER 6 -160.15 95.16 6 A THR 13 -127.82 -73.98 8 A LEU 9 -95.13 37.87 9 A LEU 9 -84.74 48.23 9 A THR 13 -116.41 59.06 10 A LEU 9 -98.62 55.44 10 A ILE 10 -166.38 81.29 11 A GLU 5 -172.20 124.60 11 A LEU 9 -93.42 49.01 11 A ILE 10 -156.86 84.71 12 A LEU 9 -98.18 56.57 12 A ILE 10 -164.38 77.90 18 A GLU 5 -156.82 88.62 19 A GLU 5 -161.10 99.52 20 A SER 6 -160.26 89.69 20 A ILE 10 -152.65 85.12 20 A THR 13 -91.25 -65.75 Solution structure of the lactam analogue EDap of HIV gp41 600-612 loop. 1 N N covale 1.342 both A ACE 1 A C ACE 1 1_555 A ILE 2 A N ILE 2 1_555 covale 1.353 both A ILE 10 A C ILE 10 1_555 A SET 11 A N SET 11 1_555 covale 1.353 one A SET 11 A CB SET 11 1_555 A THR 12 A N THR 12 1_555 VIRAL PROTEIN cyclic peptide, gp41, HIV, lactam bond, pseudopeptide., Viral protein ENV_HV1BN UNP 1 591 P12488 IWGCSGKLICTTA 591 603 1JCP 2 14 P12488 A 1 2 14 1 acetylation ACE 1 1JCP A P12488 UNP 1 1 CYS engineered mutation GLU 5 1JCP A P12488 UNP 594 5 1 CYS engineered mutation SET 11 1JCP A P12488 UNP 600 11 BINDING SITE FOR RESIDUE ACE A 1 A ACE 1 Software 2 A THR 13 A THR 13 2 1_555 A ALA 14 A ALA 14 2 1_555