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 90 90 90 1 1 1 C2 H4 O 44.053 ACETYL GROUP non-polymer C3 H7 N O2 89.093 y ALANINE L-peptide linking C4 H9 N O3 119.119 (3R)-3-AMINO-4-HYDROXYBUTANOIC ACID D-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 C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking N 1 N C N 2 N O N 3 N C N 4 N H N 5 N H N 6 N H N 7 N H N 8 N N N 9 S C N 10 N C N 11 N O N 12 N C N 13 N O N 14 N H N 15 N H N 16 N H N 17 N H N 18 N H N 19 N H N 20 N H N 21 N N N 22 N O N 23 N C N 24 R C N 25 N C N 26 N C N 27 N O N 28 N O N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N N N 39 R C N 40 N C N 41 N O N 42 N C N 43 N S N 44 N O N 45 N H N 46 N H N 47 N H N 48 N H N 49 N H N 50 N H N 51 N H N 52 N N N 53 N C N 54 N C N 55 N O N 56 N O N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N N N 63 S C N 64 N C N 65 N O N 66 S C N 67 N C N 68 N C N 69 N C N 70 N O N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N H N 80 N H N 81 N H N 82 N H N 83 N H N 84 N N N 85 S C N 86 N C N 87 N O N 88 N C N 89 N C N 90 N C N 91 N C N 92 N O N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N N N 107 S C N 108 N C N 109 N O N 110 N C N 111 N C N 112 N C N 113 N C N 114 N N N 115 N O N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N N N 132 S C N 133 N C N 134 N O N 135 N C N 136 N O N 137 N O N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N N N 146 S C N 147 N C N 148 N O N 149 R C N 150 N O N 151 N C N 152 N O N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N N N 163 S C N 164 N C N 165 N O N 166 N C Y 167 N C Y 168 N C Y 169 N C Y 170 N N Y 171 N C Y 172 N C Y 173 N C Y 174 N C Y 175 N C N 176 N O N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 1 N doub N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N doub N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N doub N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N doub N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N doub N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N doub N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N doub N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N doub N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N doub N 159 N sing N 160 N sing N 161 N sing N 162 N sing Y 163 N doub Y 164 N sing Y 165 N sing N 166 N sing Y 167 N doub Y 168 N sing Y 169 N sing N 170 N sing Y 171 N sing Y 172 N doub N 173 N sing Y 174 N doub N 175 N sing Y 176 N sing N 177 N sing N 178 N sing N 179 N sing 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/pdb1j8n/pdb pdb_00001j8n 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 x-ray 1 1.0 1393.694 HIV1 GP41 HSER analogue peptide Ace-Ile-Trp-Gly-Cys-beta3Ser-Gly-Lys-Leu-Ile-Cys-Thr-Thr-Ala 1 syn polymer no yes (ACE)IWGC(B3S)GKLICTTA XIWGCSGKLICTTA A polypeptide(L) n n n n n n n n n n n n n n pdbx_nmr_software pdbx_nmr_spectrometer struct_conn struct_ref_seq_dif database_2 struct_ref_seq_dif struct_site atom_site chem_comp_atom chem_comp_bond pdbx_validate_main_chain_plane pdbx_validate_peptide_omega pdbx_validate_rmsd_angle pdbx_validate_torsion repository Initial release Version format compliance Version format compliance Other Data collection Database references Derived calculations Database references Derived calculations Atomic model Data collection 1 0 2003-07-01 1 1 2008-04-27 1 2 2011-07-13 1 3 2011-10-05 1 4 2020-06-24 1 5 2021-10-27 2 0 2023-11-15 _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model _struct_ref_seq_dif.details _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _atom_site.auth_atom_id _atom_site.label_atom_id 1IM7 entry contains the parent peptide coordinates. RCSB Y RCSB 2001-05-22 REL REL THE PARENT SEQUENCE IWGCSGKLICTTA OCCURS IN HIV GP41 PROTEIN. This analogue contains a modified residue BSE which is a beta3-Ser (i.e. with an additional CH2 between NH and Calpha). sample THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES. NOESY EXPERIMENTS WITH MIXING TIMES FROM 80MS TO 800MS WERE RECORDED IN ORDER TO DEFINE THE BEST CONDITIONS IN ORDER TO AVOID SPIN DIFFUSION. target function 50 27 2D NOESY DQF-COSY 2D NOESY ambient 298 K 50 INITIAL RANDOM STRUCTURES WERE CALCULATED USING SIMULATED ANNEALING IN DYANA SOFTWARE. REFINEMENT WAS DONE WITH 500 STEPS RESTRAINED MINIMIZATION, 35PS MD IN VACUO AT 300K FOR EQUILIBRATION, 200PS MD UNDER NMR RESTRAINTS, AND 750PS CONJUGATED GRADIENT EM USING DISCOVER MODULE OF MSI SOFTWARE. torsion angle dynamics , molecular dynamics, energy minimization 1 lowest energy 2mM peptide ; 500ul DMSO-D6 DMSO-D6 4mM peptide ; 500ul DMSO-D6 DMSO-D6 Bruker GMBH collection XwinNMR 2.6 Bartels C., Xia T., Billeter M., Guentert P. and Wuethrich K., (1995)J. Biomolecular NMR 5, 1-10 data analysis XEASY 1.2 Guentert P., Mumenthaler C., Wuethrich K. 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 CYS 5 n 5 CYS 5 A BSE 6 n 6 B3S 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 CYS 11 n 11 CYS 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 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 18 A A O H GLY LEU 7 9 1.60 23 A A O H B3S LYS 6 8 1.59 1 A B3S 6 -16.02 4 A B3S 6 -15.32 6 A B3S 6 -16.10 7 A B3S 6 10.74 8 A B3S 6 -13.62 9 A B3S 6 -13.41 10 A B3S 6 10.13 11 A B3S 6 -13.68 12 A B3S 6 11.36 13 A B3S 6 10.05 14 A B3S 6 -15.57 15 A B3S 6 12.50 16 A B3S 6 -11.36 17 A B3S 6 10.63 18 A B3S 6 10.95 19 A B3S 6 13.42 20 A B3S 6 13.17 21 A B3S 6 11.78 22 A B3S 6 -16.93 24 A B3S 6 -15.96 25 A B3S 6 10.41 26 A B3S 6 -10.99 27 A B3S 6 -15.29 1 A A B3S GLY 6 7 144.55 4 A A B3S GLY 6 7 145.68 6 A A B3S GLY 6 7 144.37 8 A A B3S GLY 6 7 149.10 9 A A B3S GLY 6 7 149.54 11 A A B3S GLY 6 7 148.97 14 A A B3S GLY 6 7 145.32 19 A A B3S GLY 6 7 -149.73 22 A A B3S GLY 6 7 143.26 24 A A B3S GLY 6 7 144.59 27 A A B3S GLY 6 7 145.74 2 -22.68 2.00 116.20 93.52 A A A CA C N B3S B3S GLY 6 6 7 Y 3 -27.35 2.00 116.20 88.85 A A A CA C N B3S B3S GLY 6 6 7 Y 5 -23.98 2.00 116.20 92.22 A A A CA C N B3S B3S GLY 6 6 7 Y 7 -20.77 2.00 116.20 95.43 A A A CA C N B3S B3S GLY 6 6 7 Y 8 -14.74 2.00 116.20 101.46 A A A CA C N B3S B3S GLY 6 6 7 Y 9 -15.37 2.00 116.20 100.83 A A A CA C N B3S B3S GLY 6 6 7 Y 10 -22.22 2.00 116.20 93.98 A A A CA C N B3S B3S GLY 6 6 7 Y 11 -14.43 2.00 116.20 101.77 A A A CA C N B3S B3S GLY 6 6 7 Y 12 -19.34 2.00 116.20 96.86 A A A CA C N B3S B3S GLY 6 6 7 Y 13 -22.37 2.00 116.20 93.83 A A A CA C N B3S B3S GLY 6 6 7 Y 15 -16.36 2.00 116.20 99.84 A A A CA C N B3S B3S GLY 6 6 7 Y 16 -20.88 2.00 116.20 95.32 A A A CA C N B3S B3S GLY 6 6 7 Y 17 -21.16 2.00 116.20 95.04 A A A CA C N B3S B3S GLY 6 6 7 Y 18 -20.50 2.00 116.20 95.70 A A A CA C N B3S B3S GLY 6 6 7 Y 19 -13.37 2.00 116.20 102.83 A A A CA C N B3S B3S GLY 6 6 7 Y 20 -14.07 2.00 116.20 102.13 A A A CA C N B3S B3S GLY 6 6 7 Y 21 -18.41 2.00 116.20 97.79 A A A CA C N B3S B3S GLY 6 6 7 Y 23 -29.05 2.00 116.20 87.15 A A A CA C N B3S B3S GLY 6 6 7 Y 25 -21.56 2.00 116.20 94.64 A A A CA C N B3S B3S GLY 6 6 7 Y 26 -21.68 2.00 116.20 94.52 A A A CA C N B3S B3S GLY 6 6 7 Y 1 A B3S 6 -114.89 -3.42 1 A LYS 8 -90.16 41.23 1 A LEU 9 -107.17 -65.56 1 A ILE 10 -151.41 81.47 1 A THR 13 -165.06 89.27 2 A B3S 6 -101.74 -22.54 2 A LEU 9 -165.29 -43.02 2 A THR 12 -163.75 116.35 2 A THR 13 -165.13 101.07 3 A LEU 9 -165.02 -43.57 3 A THR 13 -162.73 -81.66 4 A B3S 6 -106.95 -5.80 4 A LYS 8 -68.70 66.68 4 A LEU 9 -165.05 -43.51 4 A THR 13 -157.45 -78.22 5 A B3S 6 -86.15 33.15 5 A LYS 8 -69.00 66.60 5 A LEU 9 -153.60 -46.30 5 A THR 13 -165.11 107.66 6 A B3S 6 -122.41 -3.40 6 A LYS 8 -90.57 40.23 6 A LEU 9 -108.44 -68.15 6 A ILE 10 -166.06 110.31 6 A THR 13 -162.14 -79.86 7 A B3S 6 -104.84 -10.50 7 A LEU 9 -165.37 -43.04 7 A THR 13 -162.42 -83.19 8 A B3S 6 -120.01 33.89 8 A LYS 8 -69.10 63.82 8 A LEU 9 -132.75 -45.07 8 A ILE 10 -165.12 114.18 8 A THR 13 -165.13 110.65 9 A B3S 6 -111.56 14.40 9 A LEU 9 -130.78 -45.18 9 A ILE 10 -165.21 113.80 10 A B3S 6 -104.11 -21.76 10 A LEU 9 -165.54 -42.33 10 A ILE 10 -162.95 112.76 10 A THR 13 -165.15 106.55 11 A B3S 6 -119.04 34.79 11 A LYS 8 -68.66 66.26 11 A LEU 9 -136.13 -45.34 11 A ILE 10 -165.08 114.25 11 A THR 13 -157.41 -78.21 12 A TRP 3 -160.08 96.82 12 A B3S 6 -112.03 -2.19 12 A LEU 9 -165.75 -42.50 12 A ILE 10 -165.05 114.92 12 A THR 13 -161.94 -85.78 13 A B3S 6 -156.51 57.24 13 A LYS 8 -95.90 51.84 13 A LEU 9 -166.12 -42.86 13 A ILE 10 -165.63 112.94 13 A THR 13 -162.32 106.29 14 A B3S 6 -138.43 -13.60 14 A LEU 9 -167.16 -72.33 14 A THR 13 -162.44 -84.61 15 A B3S 6 -64.34 86.07 15 A LEU 9 -150.98 -68.49 15 A ILE 10 -151.21 87.95 15 A THR 13 -165.11 109.55 16 A TRP 3 -95.08 36.97 16 A B3S 6 -125.62 37.18 16 A LEU 9 -165.74 -50.84 16 A CYS 11 -86.08 48.33 16 A THR 13 -157.38 -78.23 17 A TRP 3 -162.51 37.43 17 A CYS 5 -40.59 104.25 17 A B3S 6 -105.96 1.23 17 A LEU 9 -153.93 -45.44 17 A THR 13 -163.44 94.92 18 A B3S 6 -108.30 -13.73 18 A LEU 9 -165.86 -51.64 18 A CYS 11 -87.91 47.17 18 A THR 13 -161.31 79.64 19 A B3S 6 -80.52 103.91 19 A LEU 9 -165.40 -42.67 19 A CYS 11 -94.02 30.69 19 A THR 13 -165.07 88.49 20 A B3S 6 -71.54 95.62 20 A LYS 8 -80.59 48.07 20 A LEU 9 -138.13 -55.40 20 A ILE 10 -153.02 81.02 20 A THR 13 -162.03 98.23 21 A B3S 6 -56.67 92.05 21 A LEU 9 -153.57 -71.21 21 A ILE 10 -151.74 84.95 21 A THR 13 -164.73 108.70 22 A B3S 6 -42.50 -7.52 22 A THR 13 -165.09 95.53 23 A B3S 6 -108.11 -58.10 23 A LEU 9 -165.06 -43.33 23 A THR 13 -157.41 -78.23 24 A TRP 3 -144.48 38.21 24 A B3S 6 -103.86 -4.86 24 A LYS 8 -90.14 39.89 24 A ILE 10 -167.06 115.58 24 A THR 13 -163.73 108.62 25 A B3S 6 -109.33 -22.37 25 A LYS 8 -68.82 66.54 25 A LEU 9 -165.45 -40.85 25 A ILE 10 -166.83 116.67 25 A THR 13 -162.14 -79.50 26 A B3S 6 -110.10 -58.02 26 A LEU 9 -166.54 -68.27 26 A ILE 10 -165.78 112.93 26 A THR 13 -165.16 109.59 27 A B3S 6 -137.76 -11.99 27 A LEU 9 -167.84 -51.77 27 A THR 13 -160.03 101.36 Solution structure of beta3-analogue peptide corresponding to the gp41 600-612 loop of HIV. 1 N N disulf 2.100 A CYS 5 A SG CYS 5 1_555 A CYS 11 A SG CYS 11 1_555 covale 1.325 both A ACE 1 A C ACE 1 1_555 A ILE 2 A N ILE 2 1_555 covale 1.337 both A CYS 5 A C CYS 5 1_555 A B3S 6 A N B3S 6 1_555 covale 1.326 both A B3S 6 A C B3S 6 1_555 A GLY 7 A N GLY 7 1_555 VIRAL PROTEIN beta peptide, gp41, cyclic peptide, Viral protein ENV_HV1BN UNP 1 591 P12488 IWGCSGKLICTTA 591 603 1J8N 2 14 P12488 A 1 2 14 1 acetylation ACE 1 1J8N A P12488 UNP 1 1 SER engineered mutation B3S 6 1J8N A P12488 UNP 595 6 BINDING SITE FOR RESIDUE ACE A 1 A ACE 1 Software 2 A ILE 2 A ILE 2 2 1_555 A B3S 6 A B3S 6 2 1_555