0.023907 0.013803 0.000000 0.000000 0.027605 0.000000 0.000000 0.000000 0.011790 0.00000 0.00000 0.00000 Eckert, D.M. Malashkevich, V.N. Hong, L.H. Carr, P.A. Kim, P.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 41.829 41.829 84.817 C2 H4 O 44.053 ACETYL GROUP non-polymer C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking Cl -1 35.453 CHLORIDE ION non-polymer C3 H7 N O2 89.093 D-ALANINE D-peptide linking C6 H15 N4 O2 1 175.209 D-ARGININE D-peptide linking C3 H7 N O2 S 121.158 D-CYSTEINE D-peptide linking C5 H9 N O4 147.129 D-GLUTAMIC ACID D-peptide linking C6 H10 N3 O2 1 156.162 D-HISTIDINE D-peptide linking C6 H13 N O2 131.173 D-LEUCINE D-peptide linking C11 H12 N2 O2 204.225 D-TRYPTOPHAN D-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE 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 H2 O 18.015 WATER non-polymer 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 C5 H11 N O2 S 149.211 y METHIONINE 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 C5 H11 N O2 117.146 y VALINE L-peptide linking US Cell(Cambridge,Mass.) CELLB5 0998 0092-8674 99 103 115 10.1016/S0092-8674(00)80066-5 10520998 Inhibiting HIV-1 entry: discovery of D-peptide inhibitors that target the gp41 coiled-coil pocket. 1999 UK J.Mol.Biol. JMOBAK 0070 0022-2836 284 859 865 Crystal structure of GCN4-pIQI, a trimeric coiled-coil with buried polar residues. 1998 US Cell(Cambridge,Mass.) CELLB5 0998 0092-8674 89 15613 15617 Core structure of gp41 from the HIV envelope glycoprotein 1997 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 IMAGE PLATE 1999-03-24 RIGAKU RAXIS MAD M x-ray 1 1.1197 1.0 1.1393 1.0 1.1403 1.0 1.1399 1.0 X4A NSLS 1.1197, 1.1393, 1.1403, 1.1399 SYNCHROTRON NSLS BEAMLINE X4A 5468.566 FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GCN4-PIQI HYDROPHOBIC POCKET 1 man polymer 1859.119 D-PEPTIDE INHIBITOR 1 syn polymer 35.453 CHLORIDE ION 1 syn non-polymer 18.015 water 150 nat water IQN17 D10-P1 no yes (ACE)RMKQIEDKIEEIESKQKKIENEIARIKKLLQLTVWGIKQLQARIL XRMKQIEDKIEEIESKQKKIENEIARIKKLLQLTVWGIKQLQARIL A polypeptide(L) no yes (ACE)G(DAL)(DCY)(DGL)(DAL)(DAR)(DHI)(DAR)(DGL)(DTR)(DAL)(DTR)(DLE)(DCY)(DAL) (DAL) XGACEARHREWAWLCAA D polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n baker's yeast, Saccharomyces, Lentivirus , , sample 4932,12721 Saccharomyces cerevisiae, Human immunodeficiency virus 1 2.7 53.7 VAPOR DIFFUSION, HANGING DROP 5.6 10% PEG 4000 0.1 M SODIUM CITRATE 20% 2-PROPANOL, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K 293 repository Initial release Version format compliance Atomic model Database references Derived calculations Non-polymer description Structure summary Version format compliance 1 0 1999-10-13 1 1 2008-04-27 1 2 2011-07-13 RCSB Y RCSB 1999-09-06 REL CL CHLORIDE ION HOH water THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED sample CL 1 3 CL CL 1001 A WAT 1 4 HOH HOH 1002 A WAT 2 4 HOH HOH 1003 A WAT 3 4 HOH HOH 1004 A WAT 4 4 HOH HOH 1005 A WAT 5 4 HOH HOH 1006 A WAT 6 4 HOH HOH 1007 A WAT 7 4 HOH HOH 1008 A WAT 8 4 HOH HOH 1009 A WAT 9 4 HOH HOH 1010 A WAT 10 4 HOH HOH 1011 A WAT 11 4 HOH HOH 1012 A WAT 12 4 HOH HOH 1013 A WAT 13 4 HOH HOH 1014 A WAT 14 4 HOH HOH 1015 A WAT 15 4 HOH HOH 1016 A WAT 16 4 HOH HOH 1017 A WAT 17 4 HOH HOH 1018 A WAT 18 4 HOH HOH 1019 A WAT 19 4 HOH HOH 1020 A WAT 20 4 HOH HOH 1021 A WAT 21 4 HOH HOH 1022 A WAT 22 4 HOH HOH 1023 A WAT 23 4 HOH HOH 1024 A WAT 24 4 HOH HOH 1025 A WAT 25 4 HOH HOH 1026 A WAT 26 4 HOH HOH 1027 A WAT 28 4 HOH HOH 1028 A WAT 29 4 HOH HOH 1029 A WAT 30 4 HOH HOH 1030 A WAT 31 4 HOH HOH 1031 A WAT 32 4 HOH HOH 1032 A WAT 33 4 HOH HOH 1033 A WAT 34 4 HOH HOH 1034 A WAT 35 4 HOH HOH 1035 A WAT 36 4 HOH HOH 1036 A WAT 37 4 HOH HOH 1037 A WAT 38 4 HOH HOH 1038 A WAT 39 4 HOH HOH 1039 A WAT 40 4 HOH HOH 1040 A WAT 41 4 HOH HOH 1041 A WAT 42 4 HOH HOH 1042 A WAT 43 4 HOH HOH 1043 A WAT 44 4 HOH HOH 1044 A WAT 45 4 HOH HOH 1045 A WAT 46 4 HOH HOH 1046 A WAT 48 4 HOH HOH 1047 A WAT 49 4 HOH HOH 1048 A WAT 50 4 HOH HOH 1049 A WAT 51 4 HOH HOH 1050 A WAT 53 4 HOH HOH 1051 A WAT 54 4 HOH HOH 1052 A WAT 55 4 HOH HOH 1053 A WAT 57 4 HOH HOH 1054 A WAT 58 4 HOH HOH 1055 A WAT 59 4 HOH HOH 1056 A WAT 60 4 HOH HOH 1057 A WAT 61 4 HOH HOH 1058 A WAT 62 4 HOH HOH 1059 A WAT 63 4 HOH HOH 1060 A WAT 64 4 HOH HOH 1061 A WAT 66 4 HOH HOH 1062 A WAT 68 4 HOH HOH 1063 A WAT 69 4 HOH HOH 1064 A WAT 70 4 HOH HOH 1065 A WAT 76 4 HOH HOH 1066 A WAT 77 4 HOH HOH 1067 A WAT 80 4 HOH HOH 1068 A WAT 90 4 HOH HOH 1069 A WAT 91 4 HOH HOH 1070 A WAT 92 4 HOH HOH 1071 A WAT 93 4 HOH HOH 1072 A WAT 94 4 HOH HOH 1073 A WAT 95 4 HOH HOH 1074 A WAT 96 4 HOH HOH 1075 A WAT 97 4 HOH HOH 1076 A WAT 98 4 HOH HOH 1077 A WAT 99 4 HOH HOH 1078 A WAT 100 4 HOH HOH 1079 A WAT 101 4 HOH HOH 1080 A WAT 102 4 HOH HOH 1081 A WAT 103 4 HOH HOH 1082 A WAT 104 4 HOH HOH 1083 A WAT 105 4 HOH HOH 1084 A WAT 106 4 HOH HOH 1085 A WAT 107 4 HOH HOH 1086 A WAT 108 4 HOH HOH 1087 A WAT 109 4 HOH HOH 1088 A WAT 110 4 HOH HOH 1089 A WAT 114 4 HOH HOH 1090 A WAT 115 4 HOH HOH 1091 A WAT 117 4 HOH HOH 1092 A WAT 118 4 HOH HOH 1093 A WAT 119 4 HOH HOH 1094 A WAT 120 4 HOH HOH 1095 A WAT 121 4 HOH HOH 1096 A WAT 122 4 HOH HOH 1097 A WAT 123 4 HOH HOH 1098 A WAT 124 4 HOH HOH 1099 A WAT 125 4 HOH HOH 1100 A WAT 127 4 HOH HOH 1101 A WAT 128 4 HOH HOH 1102 A WAT 129 4 HOH HOH 1103 A WAT 130 4 HOH HOH 1104 A WAT 131 4 HOH HOH 1105 A WAT 132 4 HOH HOH 1106 A WAT 133 4 HOH HOH 1107 A WAT 134 4 HOH HOH 1108 A WAT 135 4 HOH HOH 1109 A WAT 136 4 HOH HOH 1110 A WAT 137 4 HOH HOH 1111 A WAT 138 4 HOH HOH 1112 A WAT 139 4 HOH HOH 1113 A WAT 144 4 HOH HOH 1114 A WAT 145 4 HOH HOH 1115 A WAT 146 4 HOH HOH 1116 A WAT 149 4 HOH HOH 1117 A WAT 150 4 HOH HOH 1118 A WAT 47 4 HOH HOH 47 D WAT 52 4 HOH HOH 52 D WAT 56 4 HOH HOH 56 D WAT 65 4 HOH HOH 65 D WAT 67 4 HOH HOH 67 D WAT 71 4 HOH HOH 71 D WAT 72 4 HOH HOH 72 D WAT 73 4 HOH HOH 73 D WAT 74 4 HOH HOH 74 D WAT 75 4 HOH HOH 75 D WAT 78 4 HOH HOH 78 D WAT 79 4 HOH HOH 79 D WAT 81 4 HOH HOH 81 D WAT 82 4 HOH HOH 82 D WAT 83 4 HOH HOH 83 D WAT 84 4 HOH HOH 84 D WAT 85 4 HOH HOH 85 D WAT 86 4 HOH HOH 86 D WAT 87 4 HOH HOH 87 D WAT 88 4 HOH HOH 88 D WAT 89 4 HOH HOH 89 D WAT 111 4 HOH HOH 111 D WAT 112 4 HOH HOH 112 D WAT 113 4 HOH HOH 113 D WAT 116 4 HOH HOH 116 D WAT 126 4 HOH HOH 126 D WAT 140 4 HOH HOH 140 D WAT 141 4 HOH HOH 141 D WAT 142 4 HOH HOH 142 D WAT 143 4 HOH HOH 143 D WAT 147 4 HOH HOH 147 D WAT 148 4 HOH HOH 148 D WAT 151 4 HOH HOH 151 D ACE 0 n 1 ACE 0 A ARG 1 n 2 ARG 1 A MET 2 n 3 MET 2 A LYS 3 n 4 LYS 3 A GLN 4 n 5 GLN 4 A ILE 5 n 6 ILE 5 A GLU 6 n 7 GLU 6 A ASP 7 n 8 ASP 7 A LYS 8 n 9 LYS 8 A ILE 9 n 10 ILE 9 A GLU 10 n 11 GLU 10 A GLU 11 n 12 GLU 11 A ILE 12 n 13 ILE 12 A GLU 13 n 14 GLU 13 A SER 14 n 15 SER 14 A LYS 15 n 16 LYS 15 A GLN 16 n 17 GLN 16 A LYS 17 n 18 LYS 17 A LYS 18 n 19 LYS 18 A ILE 19 n 20 ILE 19 A GLU 20 n 21 GLU 20 A ASN 21 n 22 ASN 21 A GLU 22 n 23 GLU 22 A ILE 23 n 24 ILE 23 A ALA 24 n 25 ALA 24 A ARG 25 n 26 ARG 25 A ILE 26 n 27 ILE 26 A LYS 27 n 28 LYS 27 A LYS 28 n 29 LYS 28 A LEU 29 n 30 LEU 29 A LEU 30 n 31 LEU 30 A GLN 31 n 32 GLN 31 A LEU 32 n 33 LEU 32 A THR 33 n 34 THR 33 A VAL 34 n 35 VAL 34 A TRP 35 n 36 TRP 35 A GLY 36 n 37 GLY 36 A ILE 37 n 38 ILE 37 A LYS 38 n 39 LYS 38 A GLN 39 n 40 GLN 39 A LEU 40 n 41 LEU 40 A GLN 41 n 42 GLN 41 A ALA 42 n 43 ALA 42 A ARG 43 n 44 ARG 43 A ILE 44 n 45 ILE 44 A LEU 45 n 46 LEU 45 A ACE 0 n 1 ACE 0 D DLY 1 n 2 GLY 1 D DAL 2 n 3 DAL 2 D DCY 3 n 4 DCY 3 D DGL 4 n 5 DGL 4 D DAL 5 n 6 DAL 5 D DAR 6 n 7 DAR 6 D DHI 7 n 8 DHI 7 D DAR 8 n 9 DAR 8 D DGL 9 n 10 DGL 9 D DTR 10 n 11 DTR 10 D DAL 11 n 12 DAL 11 D DTR 12 n 13 DTR 12 D DEU 13 n 14 DLE 13 D DCY 14 n 15 DCY 14 D DAL 15 n 16 DAL 15 D DAL 16 n 17 DAL 16 D author_and_software_defined_assembly PISA,PQS 6 hexameric 9460 -115 10980 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 -0.5000000000 -0.8660254038 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 2_655 -y+1,x-y,z crystal symmetry operation 41.8290000000 0.0000000000 0.0000000000 -0.5000000000 0.8660254038 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 3_665 -x+y+1,-x+1,z crystal symmetry operation 20.9145000000 36.2249766149 0.0000000000 1 A CL 1001 C CL 1 A HOH 1020 D HOH 1 A HOH 1063 D HOH 1 A HOH 1088 D HOH 1 A HOH 1107 D HOH 1 A HOH 1109 D HOH 1 -6.14 0.50 120.30 114.16 A A A NE CZ NH2 ARG ARG ARG 43 43 43 N PROTEIN_REP_D.PARAM PROTEIN.TOP WATER_REP.PARA WATER.TOP ION.PARAM ION.TOP 29.7 3.61 1.74 0.00 3.61 0.00 -7.22 0.245 0.007 0.214 0.214 0.214 1.50 10.00 1362 14322 13549 10.0 94.6 RANDOM 646169.44 0.00 1 RESTRAINED THROUGHOUT 0.0 0.0 ENGH & HUBER FLAT MODEL 58.34 0.394 0.20 0.18 5.00 0.12 0.09 1.50 10.00 150 666 1 0 515 0.012 1.5 15.7 1.00 0.956 2.0 1.503 3.0 1.853 3.0 2.676 3.5 0.27 0.018 0.233 1.59 219 2008 6 9.8 96.1 21.6 1.5 35.0 1CZQ 14503 13604 0.0 -3 0.048 1 16.8 6.5 93.8 0.235 1.5 1.55 4.5 1 6.1 86.8 data reduction DENZO data scaling SCALEPACK phasing MLPHARE refinement CNS 0.5 FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GCN4-PIQI CRYSTAL STRUCTURE OF THE D10-P1/IQN17 COMPLEX: A D-PEPTIDE INHIBITOR OF HIV-1 ENTRY BOUND TO THE GP41 COILED-COIL POCKET. 1 N N 2 N N 3 N N 4 N N 4 N N A ARG 1 A ARG 2 HELX_P A LEU 45 A LEU 46 1 1 45 disulf 2.048 D DCY 3 B SG DCY 4 1_555 D DCY 14 B SG DCY 15 1_555 covale 1.333 A ACE 0 A C ACE 1 1_555 A ARG 1 A N ARG 2 1_555 covale 1.336 D ACE 0 B C ACE 1 1_555 D GLY 1 B N GLY 2 1_555 covale 1.327 D GLY 1 B C GLY 2 1_555 D DAL 2 B N DAL 3 1_555 covale 1.324 D DAL 2 B C DAL 3 1_555 D DCY 3 B N DCY 4 1_555 covale 1.323 D DCY 3 B C DCY 4 1_555 D DGL 4 B N DGL 5 1_555 covale 2.048 D DCY 3 B SG DCY 4 1_555 D DCY 14 B SG DCY 15 1_555 covale 1.326 D DGL 4 B C DGL 5 1_555 D DAL 5 B N DAL 6 1_555 covale 1.327 D DAL 5 B C DAL 6 1_555 D DAR 6 B N DAR 7 1_555 covale 1.324 D DAR 6 B C DAR 7 1_555 D DHI 7 B N DHI 8 1_555 covale 1.329 D DHI 7 B C DHI 8 1_555 D DAR 8 B N DAR 9 1_555 covale 1.329 D DAR 8 B C DAR 9 1_555 D DGL 9 B N DGL 10 1_555 covale 1.328 D DGL 9 B C DGL 10 1_555 D DTR 10 B N DTR 11 1_555 covale 1.332 D DTR 10 B C DTR 11 1_555 D DAL 11 B N DAL 12 1_555 covale 1.335 D DAL 11 B C DAL 12 1_555 D DTR 12 B N DTR 13 1_555 covale 1.330 D DTR 12 B C DTR 13 1_555 D DLE 13 B N DLE 14 1_555 covale 1.335 D DLE 13 B C DLE 14 1_555 D DCY 14 B N DCY 15 1_555 covale 1.329 D DCY 14 B C DCY 15 1_555 D DAL 15 B N DAL 16 1_555 covale 1.332 D DAL 15 B C DAL 16 1_555 D DAL 16 B N DAL 17 1_555 Viral protein/inhibitor ENVELOPE GLYCOPROTEIN, Viral protein-inhibitor COMPLEX U36871 GB 1 1587615 1CZQ PDB 2 1CZQ 565 581 1CZQ 29 45 1587615 A 1 30 46 0 16 1CZQ 0 16 1CZQ D 2 1 17 BINDING SITE FOR RESIDUE CL A 1001 Software 3 BINDING SITE FOR CHAIN D OF D-PEPTIDE INHIBITOR Software 34 A GLN 16 A GLN 17 3 1_555 A GLN 16 A GLN 17 3 3_665 A GLN 16 A GLN 17 3 2_655 A LEU 32 A LEU 33 34 1_555 A VAL 34 A VAL 35 34 2_655 A TRP 35 A TRP 36 34 1_555 A LYS 38 A LYS 39 34 2_655 A GLN 41 A GLN 42 34 2_655 A ARG 43 A ARG 44 34 5_556 A ARG 43 A ARG 44 34 6_656 A ILE 44 A ILE 45 34 6_656 A LEU 45 A LEU 46 34 6_656 A HOH 1057 D HOH 34 2_655 A HOH 1065 D HOH 34 2_655 A HOH 1077 D HOH 34 2_655 A HOH 1083 D HOH 34 5_556 A HOH 1086 D HOH 34 6_656 A HOH 1106 D HOH 34 4_546 A HOH 1114 D HOH 34 4_546 D HOH 47 E HOH 34 1_555 D HOH 52 E HOH 34 1_555 D HOH 65 E HOH 34 1_555 D HOH 67 E HOH 34 1_555 D HOH 71 E HOH 34 1_555 D HOH 72 E HOH 34 1_555 D HOH 73 E HOH 34 1_555 D HOH 74 E HOH 34 1_555 D HOH 79 E HOH 34 1_555 D HOH 83 E HOH 34 1_555 D HOH 85 E HOH 34 1_555 D HOH 86 E HOH 34 1_555 D HOH 87 E HOH 34 1_555 D HOH 88 E HOH 34 1_555 D HOH 111 E HOH 34 1_555 D HOH 140 E HOH 34 1_555 D HOH 142 E HOH 34 1_555 D HOH 143 E HOH 34 1_555 150 P 3 2 1