0.019268 0.000000 0.000000 0.000000 0.019268 0.000000 0.000000 0.000000 0.015773 0.00000 0.00000 0.00000 Vajdos, F.F. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 51.900 51.900 63.400 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 C3 H7 N O2 S 121.158 y CYSTEINE L-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 C6 H10 N3 O2 1 156.162 y HISTIDINE L-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 C5 H11 N O2 Se 196.106 n SELENOMETHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE 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 C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US Protein Sci. PRCIEI 0795 0961-8368 6 2297 2307 9385632 Crystal structure of cyclophilin A complexed with a binding site peptide from the HIV-1 capsid protein. 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 AREA DETECTOR 1996-06 MARRESEARCH SI(111) M x-ray 1 0.9794 1.0 X12C NSLS 0.9794 SYNCHROTRON NSLS BEAMLINE X12C 18092.887 CYCLOPHILIN A 5.2.1.8 SELENO-METHIONINE SUBSTITUTED 1 man polymer 565.642 PEPTIDE FROM THE HIV-1 CAPSID PROTEIN 1 man polymer 18.015 water 52 nat water no yes VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGF(MSE)CQGGDFTRHNGTGGKS IYGEKFEDENFILKHTGPGILS(MSE)ANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEG(MSE)NIVEA(MSE)ERF GSRNGKTSKKITIADCGQLE VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGE KFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADC GQLE A polypeptide(L) no no HAGPIA HAGPIA B 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 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 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 human Homo Escherichia sample CYTOPLASM CYCLOPHILIN 9606 Homo sapiens CYCLOPHILIN 562 Escherichia coli 1 2.29 46.22 8.4 pH 8.4 repository Initial release Version format compliance Version format compliance 1 0 1998-03-18 1 1 2008-03-24 1 2 2011-07-13 Y 1997-10-04 REL REL HOH water HOH 201 3 HOH HOH 201 A HOH 202 3 HOH HOH 202 A HOH 203 3 HOH HOH 203 A HOH 204 3 HOH HOH 204 A HOH 205 3 HOH HOH 205 A HOH 206 3 HOH HOH 206 A HOH 207 3 HOH HOH 207 A HOH 208 3 HOH HOH 208 A HOH 209 3 HOH HOH 209 A HOH 210 3 HOH HOH 210 A HOH 211 3 HOH HOH 211 A HOH 212 3 HOH HOH 212 A HOH 214 3 HOH HOH 214 A HOH 215 3 HOH HOH 215 A HOH 216 3 HOH HOH 216 A HOH 217 3 HOH HOH 217 A HOH 218 3 HOH HOH 218 A HOH 219 3 HOH HOH 219 A HOH 220 3 HOH HOH 220 A HOH 221 3 HOH HOH 221 A HOH 222 3 HOH HOH 222 A HOH 223 3 HOH HOH 223 A HOH 224 3 HOH HOH 224 A HOH 225 3 HOH HOH 225 A HOH 226 3 HOH HOH 226 A HOH 227 3 HOH HOH 227 A HOH 228 3 HOH HOH 228 A HOH 229 3 HOH HOH 229 A HOH 230 3 HOH HOH 230 A HOH 231 3 HOH HOH 231 A HOH 232 3 HOH HOH 232 A HOH 233 3 HOH HOH 233 A HOH 234 3 HOH HOH 234 A HOH 235 3 HOH HOH 235 A HOH 236 3 HOH HOH 236 A HOH 237 3 HOH HOH 237 A HOH 238 3 HOH HOH 238 A HOH 239 3 HOH HOH 239 A HOH 240 3 HOH HOH 240 A HOH 241 3 HOH HOH 241 A HOH 242 3 HOH HOH 242 A HOH 243 3 HOH HOH 243 A HOH 244 3 HOH HOH 244 A HOH 245 3 HOH HOH 245 A HOH 246 3 HOH HOH 246 A HOH 248 3 HOH HOH 248 A HOH 249 3 HOH HOH 249 A HOH 250 3 HOH HOH 250 A HOH 251 3 HOH HOH 251 A HOH 252 3 HOH HOH 252 A HOH 213 3 HOH HOH 213 B HOH 247 3 HOH HOH 247 B VAL 1002 n 1 VAL 1002 A ASN 1003 n 2 ASN 1003 A PRO 1004 n 3 PRO 1004 A THR 1005 n 4 THR 1005 A VAL 1006 n 5 VAL 1006 A PHE 1007 n 6 PHE 1007 A PHE 1008 n 7 PHE 1008 A ASP 1009 n 8 ASP 1009 A ILE 1010 n 9 ILE 1010 A ALA 1011 n 10 ALA 1011 A VAL 1012 n 11 VAL 1012 A ASP 1013 n 12 ASP 1013 A GLY 1014 n 13 GLY 1014 A GLU 1015 n 14 GLU 1015 A PRO 1016 n 15 PRO 1016 A LEU 1017 n 16 LEU 1017 A GLY 1018 n 17 GLY 1018 A ARG 1019 n 18 ARG 1019 A VAL 1020 n 19 VAL 1020 A SER 1021 n 20 SER 1021 A PHE 1022 n 21 PHE 1022 A GLU 1023 n 22 GLU 1023 A LEU 1024 n 23 LEU 1024 A PHE 1025 n 24 PHE 1025 A ALA 1026 n 25 ALA 1026 A ASP 1027 n 26 ASP 1027 A LYS 1028 n 27 LYS 1028 A VAL 1029 n 28 VAL 1029 A PRO 1030 n 29 PRO 1030 A LYS 1031 n 30 LYS 1031 A THR 1032 n 31 THR 1032 A ALA 1033 n 32 ALA 1033 A GLU 1034 n 33 GLU 1034 A ASN 1035 n 34 ASN 1035 A PHE 1036 n 35 PHE 1036 A ARG 1037 n 36 ARG 1037 A ALA 1038 n 37 ALA 1038 A LEU 1039 n 38 LEU 1039 A SER 1040 n 39 SER 1040 A THR 1041 n 40 THR 1041 A GLY 1042 n 41 GLY 1042 A GLU 1043 n 42 GLU 1043 A LYS 1044 n 43 LYS 1044 A GLY 1045 n 44 GLY 1045 A PHE 1046 n 45 PHE 1046 A GLY 1047 n 46 GLY 1047 A TYR 1048 n 47 TYR 1048 A LYS 1049 n 48 LYS 1049 A GLY 1050 n 49 GLY 1050 A SER 1051 n 50 SER 1051 A CYS 1052 n 51 CYS 1052 A PHE 1053 n 52 PHE 1053 A HIS 1054 n 53 HIS 1054 A ARG 1055 n 54 ARG 1055 A ILE 1056 n 55 ILE 1056 A ILE 1057 n 56 ILE 1057 A PRO 1058 n 57 PRO 1058 A GLY 1059 n 58 GLY 1059 A PHE 1060 n 59 PHE 1060 A MSE 1061 n 60 MSE 1061 A CYS 1062 n 61 CYS 1062 A GLN 1063 n 62 GLN 1063 A GLY 1064 n 63 GLY 1064 A GLY 1065 n 64 GLY 1065 A ASP 1066 n 65 ASP 1066 A PHE 1067 n 66 PHE 1067 A THR 1068 n 67 THR 1068 A ARG 1069 n 68 ARG 1069 A HIS 1070 n 69 HIS 1070 A ASN 1071 n 70 ASN 1071 A GLY 1072 n 71 GLY 1072 A THR 1073 n 72 THR 1073 A GLY 1074 n 73 GLY 1074 A GLY 1075 n 74 GLY 1075 A LYS 1076 n 75 LYS 1076 A SER 1077 n 76 SER 1077 A ILE 1078 n 77 ILE 1078 A TYR 1079 n 78 TYR 1079 A GLY 1080 n 79 GLY 1080 A GLU 1081 n 80 GLU 1081 A LYS 1082 n 81 LYS 1082 A PHE 1083 n 82 PHE 1083 A GLU 1084 n 83 GLU 1084 A ASP 1085 n 84 ASP 1085 A GLU 1086 n 85 GLU 1086 A ASN 1087 n 86 ASN 1087 A PHE 1088 n 87 PHE 1088 A ILE 1089 n 88 ILE 1089 A LEU 1090 n 89 LEU 1090 A LYS 1091 n 90 LYS 1091 A HIS 1092 n 91 HIS 1092 A THR 1093 n 92 THR 1093 A GLY 1094 n 93 GLY 1094 A PRO 1095 n 94 PRO 1095 A GLY 1096 n 95 GLY 1096 A ILE 1097 n 96 ILE 1097 A LEU 1098 n 97 LEU 1098 A SER 1099 n 98 SER 1099 A MSE 1100 n 99 MSE 1100 A ALA 1101 n 100 ALA 1101 A ASN 1102 n 101 ASN 1102 A ALA 1103 n 102 ALA 1103 A GLY 1104 n 103 GLY 1104 A PRO 1105 n 104 PRO 1105 A ASN 1106 n 105 ASN 1106 A THR 1107 n 106 THR 1107 A ASN 1108 n 107 ASN 1108 A GLY 1109 n 108 GLY 1109 A SER 1110 n 109 SER 1110 A GLN 1111 n 110 GLN 1111 A PHE 1112 n 111 PHE 1112 A PHE 1113 n 112 PHE 1113 A ILE 1114 n 113 ILE 1114 A CYS 1115 n 114 CYS 1115 A THR 1116 n 115 THR 1116 A ALA 1117 n 116 ALA 1117 A LYS 1118 n 117 LYS 1118 A THR 1119 n 118 THR 1119 A GLU 1120 n 119 GLU 1120 A TRP 1121 n 120 TRP 1121 A LEU 1122 n 121 LEU 1122 A ASP 1123 n 122 ASP 1123 A GLY 1124 n 123 GLY 1124 A LYS 1125 n 124 LYS 1125 A HIS 1126 n 125 HIS 1126 A VAL 1127 n 126 VAL 1127 A VAL 1128 n 127 VAL 1128 A PHE 1129 n 128 PHE 1129 A GLY 1130 n 129 GLY 1130 A LYS 1131 n 130 LYS 1131 A VAL 1132 n 131 VAL 1132 A LYS 1133 n 132 LYS 1133 A GLU 1134 n 133 GLU 1134 A GLY 1135 n 134 GLY 1135 A MSE 1136 n 135 MSE 1136 A ASN 1137 n 136 ASN 1137 A ILE 1138 n 137 ILE 1138 A VAL 1139 n 138 VAL 1139 A GLU 1140 n 139 GLU 1140 A ALA 1141 n 140 ALA 1141 A MSE 1142 n 141 MSE 1142 A GLU 1143 n 142 GLU 1143 A ARG 1144 n 143 ARG 1144 A PHE 1145 n 144 PHE 1145 A GLY 1146 n 145 GLY 1146 A SER 1147 n 146 SER 1147 A ARG 1148 n 147 ARG 1148 A ASN 1149 n 148 ASN 1149 A GLY 1150 n 149 GLY 1150 A LYS 1151 n 150 LYS 1151 A THR 1152 n 151 THR 1152 A SER 1153 n 152 SER 1153 A LYS 1154 n 153 LYS 1154 A LYS 1155 n 154 LYS 1155 A ILE 1156 n 155 ILE 1156 A THR 1157 n 156 THR 1157 A ILE 1158 n 157 ILE 1158 A ALA 1159 n 158 ALA 1159 A ASP 1160 n 159 ASP 1160 A CYS 1161 n 160 CYS 1161 A GLY 1162 n 161 GLY 1162 A GLN 1163 n 162 GLN 1163 A LEU 1164 n 163 LEU 1164 A GLU 1165 n 164 GLU 1165 A HIS 1 n 1 HIS 1 B ALA 2 n 2 ALA 2 B GLY 3 n 3 GLY 3 B PRO 4 n 4 PRO 4 B ILE 5 n 5 ILE 5 B ALA 6 n 6 ALA 6 B author_and_software_defined_assembly PISA 2 dimeric 740 -4 7490 A MSE 1061 SELENOMETHIONINE A MSE 60 MET A MSE 1100 SELENOMETHIONINE A MSE 99 MET A MSE 1136 SELENOMETHIONINE A MSE 135 MET A MSE 1142 SELENOMETHIONINE A MSE 141 MET 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 A O ARG 1055 A O ARG 54 A N GLN 1063 A N GLN 62 A O CYS 1062 A O CYS 61 A N ILE 1114 A N ILE 113 A O PHE 1113 A O PHE 112 A N SER 1099 A N SER 98 A O LEU 1098 A O LEU 97 A N GLY 1130 A N GLY 129 A O LYS 1131 A O LYS 130 A N GLU 1023 A N GLU 22 A O GLU 1015 A O GLU 14 A N VAL 1012 A N VAL 11 A O PHE 1007 A O PHE 6 A N GLY 1162 A N GLY 161 1 A VAL 1029 -113.20 70.82 1 A PRO 1030 -51.84 -76.44 1 A GLU 1043 -47.54 7.05 1 A LYS 1044 -150.96 -4.07 1 A PHE 1046 -100.62 -86.09 1 A PHE 1060 -121.01 -77.52 1 A ASN 1071 -134.86 -34.47 1 A TYR 1079 -93.09 37.54 1 A GLU 1081 -140.34 -63.00 1 A ASN 1087 -174.98 -176.81 1 A HIS 1092 -59.25 69.95 1 A ALA 1101 -101.12 77.94 1 A PRO 1105 -28.76 139.76 1 A ALA 1117 174.37 161.96 1 A PHE 1129 -147.98 -1.21 1 A SER 1147 -154.23 -152.62 PARHCSDX.PRO TOPHCSDX.PRO TIP3P.PARAMETER TIP3P.TOPOLOGY 26.5 BULK SOLVENT MODEL USED THE PROTEIN IS SELENO-METHIONINE SUBSTITUTED, BUT THE SELENO-METHIONINE RESIDUES WERE REFINED AS METHIONINES. REGARDING THE HIGH R-VALUE: THIS IS THE STRUCTURE OF THE COMPLEX REFINED IN A PSEUDO-SPACE GROUP. THE DETAILS ARE ADDRESSED EXTENSIVELY IN THE PAPER. TO SUMMARIZE HERE, THE HIGH R-VALUE FOR THIS STRUCTURE STEMS FROM THE BREAKDOWN IN PSEUDO-SYMMETRY AT HIGH RESOLUTION. 0.3370000 0.019 0.2620000 0.2620000 2.55 15.00 304 5484 5.5 99.2 RANDOM 10000000.00 0.00100 1 RESTRAINED THROUGHOUT 0.0 MAD 0.48 0.37 5.00 0.72 0.50 2.55 15.00 52 1350 40 0 1258 0.009 1.5 25.9 1.30 4.37 1.50 5.95 2.00 5.56 2.00 6.90 2.50 0.5060000 0.078 0.3810000 2.71 42 871 6 4.6 99.1 16.8 2.55 15.0 1AWS 5576 0. 0.0350000 1 19.1 97.6 2.55 2.59 0.0790000 95.7 model building X-PLOR 3.843 refinement X-PLOR 3.843 data reduction DENZO data scaling SCALEPACK phasing X-PLOR 3.843 CYCLOPHILIN A, PEPTIDE FROM THE HIV-1 CAPSID PROTEIN SECYPA COMPLEXED WITH HAGPIA (PSEUDO-SYMMETRIC MONOMER) 1 N N 2 N N 3 N N 3 N N A PRO 1030 A PRO 29 HELX_P A THR 1041 A THR 40 1 1 12 A GLU 1120 A GLU 119 HELX_P A LEU 1122 A LEU 121 5 2 3 A MSE 1136 A MSE 135 HELX_P A ARG 1144 A ARG 143 1 3 9 covale 1.338 A MSE 1061 A N MSE 60 1_555 A PHE 1060 A C PHE 59 1_555 covale 1.342 A MSE 1061 A C MSE 60 1_555 A CYS 1062 A N CYS 61 1_555 covale 1.324 A MSE 1100 A N MSE 99 1_555 A SER 1099 A C SER 98 1_555 covale 1.331 A MSE 1100 A C MSE 99 1_555 A ALA 1101 A N ALA 100 1_555 covale 1.331 A MSE 1136 A N MSE 135 1_555 A GLY 1135 A C GLY 134 1_555 covale 1.331 A MSE 1136 A C MSE 135 1_555 A ASN 1137 A N ASN 136 1_555 covale 1.336 A MSE 1142 A N MSE 141 1_555 A ALA 1141 A C ALA 140 1_555 covale 1.333 A MSE 1142 A C MSE 141 1_555 A GLU 1143 A N GLU 142 1_555 COMPLEX (ISOMERASE/PEPTIDE) COMPLEX (ISOMERASE-PEPTIDE), CYCLOPHILIN A, HIV-1 CAPSID, PSEUDO-SYMMETRY, COMPLEX (ISOMERASE-PEPTIDE) complex PPIA_HUMAN UNP 1 1 P62937 VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGE KFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADC GQLE 1AWS PDB 2 1AWS 1 164 1AWS 1002 1165 P62937 A 1 1 164 1 6 1AWS 1 6 1AWS B 2 1 6 1 MET MODIFIED RESIDUE MSE 1061 1AWS A P62937 UNP 60 60 1 MET MODIFIED RESIDUE MSE 1100 1AWS A P62937 UNP 99 99 1 MET MODIFIED RESIDUE MSE 1136 1AWS A P62937 UNP 135 135 1 MET MODIFIED RESIDUE MSE 1142 1AWS A P62937 UNP 141 141 8 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A ARG 1055 A ARG 54 A ILE 1057 A ILE 56 A MSE 1061 A MSE 60 A GLY 1064 A GLY 63 A PHE 1112 A PHE 111 A CYS 1115 A CYS 114 A ILE 1097 A ILE 96 A MSE 1100 A MSE 99 A VAL 1128 A VAL 127 A GLU 1134 A GLU 133 A GLU 1015 A GLU 14 A LEU 1024 A LEU 23 A THR 1005 A THR 4 A VAL 1012 A VAL 11 A ILE 1156 A ILE 155 A GLN 1163 A GLN 162 78 P 43