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Sequence, Chains, Asymmetric and Biological Units

Title CRYSTAL STRUCTURE OF F23, A SCORPION-TOXIN MIMIC OF CD4, IN WITH HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN AND ANTI-HIV-1 A 17B
Keywords HIV-1, GP120, YU2, SCORPION TOXIN, CD4 MIMIC, F23, ANTIBODY, PROTEIN-IMMUNE SYSTEM COMPLEX
Experiment X-ray diffraction
Number of Models  1


   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  

PDB   1YYM     released     available     available     Quaternary Structure Server  


Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   EXTERIOR MEMBRANE GLYCOPROTEIN(GP120),EXTERIOR ME GLYCOPROTEIN(GP120),EXTERIOR MEMBRANE GLYCOPROTEIN(GP120)  G 301 2341 0
2  Protein   ANTIBODY 17B LIGHT CHAIN  L 214 1647 0
3  Protein   ANTIBODY 17B HEAVY CHAIN  H 229 1722 0
4  Protein   F23, SCORPION-TOXIN MIMIC OF CD4  M 27 182 13
5  Protein   EXTERIOR MEMBRANE GLYCOPROTEIN(GP120),EXTERIOR ME GLYCOPROTEIN(GP120),EXTERIOR MEMBRANE GLYCOPROTEIN(GP120)  P 299 2325 0
6  Protein   ANTIBODY 17B LIGHT CHAIN  Q 214 1647 0
7  Protein   ANTIBODY 17B HEAVY CHAIN  R 229 1722 0
8  Protein   F23, SCORPION-TOXIN MIMIC OF CD4  S 27 182 13
9  Ligand   EXTERIOR MEMBRANE GLYCOPROTEIN(GP120),EXTERIOR ME GLYCOPROTEIN(GP120),EXTERIOR MEMBRANE GLYCOPROTEIN(GP120)  G 10 0 120
10  Ligand   F23, SCORPION-TOXIN MIMIC OF CD4  M 1 0 4
11  Ligand   EXTERIOR MEMBRANE GLYCOPROTEIN(GP120),EXTERIOR ME GLYCOPROTEIN(GP120),EXTERIOR MEMBRANE GLYCOPROTEIN(GP120)  P 9 0 116
12 Water     789 0 789
total       2349 11768 1055

Proteins
Unit 1 GLU83 VAL84 LYS85 LEU86 GLU87 ASN88 VAL89 THR90 GLU91 ASN92 PHE93 ASN94 MET95 TRP96 LYS97 ASN98 ASN99 MET100 VAL101 GLU102 GLN103 MET104 HIS105 GLU106 ASP107 ILE108 ILE109 SER110 LEU111 TRP112 ASP113 GLN114 SER115 LEU116 LYS117 PRO118 CYS119 VAL120 LYS121 LEU122 THR123 PRO124 LEU125 CYS126 VAL127 GLY128 ALA129 GLY194 SER195 CYS196 ASN197 THR198 SER199 VAL200 ILE201 THR202 GLN203 ALA204 CYS205 PRO206 LYS207 VAL208 SER209 PHE210 GLU211 PRO212 ILE213 PRO214 ILE215 HIS216 TYR217 CYS218 ALA219 PRO220 ALA221 GLY222 PHE223 ALA224 ILE225 LEU226 LYS227 CYS228 ASN229 ASP230 LYS231 LYS232 PHE233 ASN234 GLY235 THR236 GLY237 PRO238 CYS239 THR240 ASN241 VAL242 SER243 THR244 VAL245 GLN246 CYS247 THR248 HIS249 GLY250 ILE251 ARG252 PRO253 VAL254 VAL255 SER256 THR257 GLN258 LEU259 LEU260 LEU261 ASN262 GLY263 SER264 LEU265 ALA266 GLU267 GLU268 GLU269 ILE270 VAL271 ILE272 ARG273 SER274 GLU275 ASN276 PHE277 THR278 ASN279 ASN280 ALA281 LYS282 THR283 ILE284 ILE285 VAL286 GLN287 LEU288 ASN289 GLU290 SER291 VAL292 VAL293 ILE294 ASN295 CYS296 THR297 GLY298 ALA299 GLY329 HIS330 CYS331 ASN332 LEU333 SER334 LYS335 THR336 GLN337 TRP338 GLU339 ASN340 THR341 LEU342 GLU343 GLN344 ILE345 ALA346 ILE347 LYS348 LEU349 LYS350 GLU351 GLN352 PHE353 GLY354 ASN355 ASN356 LYS357 THR358 ILE359 ILE360 PHE361 ASN362 PRO363 SER364 SER365 GLY366 GLY367 ASP368 PRO369 GLU370 ILE371 VAL372 THR373 HIS374 SER375 PHE376 ASN377 CYS378 GLY379 GLY380 GLU381 PHE382 PHE383 TYR384 CYS385 ASN386 SER387 THR388 GLN389 LEU390 PHE391 THR392 TRP393 ASN394 ASP395 ARG412 ASN413 ILE414 THR415 LEU416 PRO417 CYS418 ARG419 ILE420 LYS421 GLN422 ILE423 ILE424 ASN425 MET426 TRP427 GLN428 GLU429 VAL430 GLY431 LYS432 ALA433 MET434 TYR435 ALA436 PRO437 PRO438 ILE439 ARG440 GLY441 GLN442 ILE443 ARG444 CYS445 SER446 SER447 ASN448 ILE449 THR450 GLY451 LEU452 LEU453 LEU454 THR455 ARG456 ASP457 GLY458 GLY459 LYS460 ASP461 THR462 ASN463 GLY464 THR465 GLU466 ILE467 PHE468 ARG469 PRO470 GLY471 GLY472 GLY473 ASP474 MET475 ARG476 ASP477 ASN478 TRP479 ARG480 SER481 GLU482 LEU483 TYR484 LYS485 TYR486 LYS487 VAL488 VAL489 LYS490 ILE491 GLU492
Unit 2 ASP1 ILE2 VAL3 MET4 THR5 GLN6 SER7 PRO8 ALA9 THR10 LEU11 SER12 VAL13 SER14 PRO15 GLY16 GLU17 ARG18 ALA19 THR20 LEU21 SER22 CYS23 ARG24 ALA25 SER26 GLU27 SER28 VAL29 SER30 SER31 ASP32 LEU33 ALA34 TRP35 TYR36 GLN37 GLN38 LYS39 PRO40 GLY41 GLN42 ALA43 PRO44 ARG45 LEU46 LEU47 ILE48 TYR49 GLY50 ALA51 SER52 THR53 ARG54 ALA55 THR56 GLY57 VAL58 PRO59 ALA60 ARG61 PHE62 SER63 GLY64 SER65 GLY66 SER67 GLY68 ALA69 GLU70 PHE71 THR72 LEU73 THR74 ILE75 SER76 SER77 LEU78 GLN79 SER80 GLU81 ASP82 PHE83 ALA84 VAL85 TYR86 TYR87 CYS88 GLN89 GLN90 TYR91 ASN92 ASN93 TRP94 PRO95 PRO95A ARG95B TYR96 THR97 PHE98 GLY99 GLN100 GLY101 THR102 ARG103 LEU104 GLU105 ILE106 LYS107 ARG108 THR109 VAL110 ALA111 ALA112 PRO113 SER114 VAL115 PHE116 ILE117 PHE118 PRO119 PRO120 SER121 ASP122 GLU123 GLN124 LEU125 LYS126 SER127 GLY128 THR129 ALA130 SER131 VAL132 VAL133 CYS134 LEU135 LEU136 ASN137 ASN138 PHE139 TYR140 PRO141 ARG142 GLU143 ALA144 LYS145 VAL146 GLN147 TRP148 LYS149 VAL150 ASP151 ASN152 ALA153 LEU154 GLN155 SER156 GLY157 ASN158 SER159 GLN160 GLU161 SER162 VAL163 THR164 GLU165 GLN166 ASP167 SER168 LYS169 ASP170 SER171 THR172 TYR173 SER174 LEU175 SER176 SER177 THR178 LEU179 THR180 LEU181 SER182 LYS183 ALA184 ASP185 TYR186 GLU187 LYS188 HIS189 LYS190 VAL191 TYR192 ALA193 CYS194 GLU195 VAL196 THR197 HIS198 GLN199 GLY200 LEU201 SER202 SER203 PRO204 VAL205 THR206 LYS207 SER208 PHE209 ASN210 ARG211 GLY212
Unit 3 GLU1 VAL2 GLN3 LEU4 VAL5 GLU6 SER7 GLY8 ALA9 GLU10 VAL11 LYS12 LYS13 PRO14 GLY15 SER16 SER17 VAL18 LYS19 VAL20 SER21 CYS22 LYS23 ALA24 SER25 GLY26 ASP27 THR28 PHE29 ILE30 ARG31 TYR32 SER33 PHE34 THR35 TRP36 VAL37 ARG38 GLN39 ALA40 PRO41 GLY42 GLN43 GLY44 LEU45 GLU46 TRP47 MET48 GLY49 ARG50 ILE51 ILE52 THR52A ILE53 LEU54 ASP55 VAL56 ALA57 HIS58 TYR59 ALA60 PRO61 HIS62 LEU63 GLN64 GLY65 ARG66 VAL67 THR68 ILE69 THR70 ALA71 ASP72 LYS73 SER74 THR75 SER76 THR77 VAL78 TYR79 LEU80 GLU81 LEU82 ARG82A ASN82B LEU82C ARG83 SER84 ASP85 ASP86 THR87 ALA88 VAL89 TYR90 PHE91 CYS92 ALA93 GLY94 VAL95 TYR96 GLU97 GLY98 GLU99 ALA100 ASP100A GLU100B GLY100C GLU100D TYR100E ASP100F ASN100G ASN100H GLY100I PHE100J LEU100K LYS101 HIS102 TRP103 GLY104 GLN105 GLY106 THR107 LEU108 VAL109 THR110 VAL111 SER112 SER113 ALA114 SER115 THR116 LYS117 GLY118 PRO119 SER120 VAL121 PHE122 PRO123 LEU124 ALA125 PRO126 SER127 SER128 LYS129 SER130 THR131 SER132 GLY133 GLY134 THR135 ALA136 ALA137 LEU138 GLY139 CYS140 LEU141 VAL142 LYS143 ASP144 TYR145 PHE146 PRO147 GLU148 PRO149 VAL150 THR151 VAL152 SER153 TRP154 ASN155 SER156 GLY157 ALA158 LEU159 THR160 SER161 GLY162 VAL163 HIS164 THR165 PHE166 PRO167 ALA168 VAL169 LEU170 GLN171 SER172 SER173 GLY174 LEU175 TYR176 SER177 LEU178 SER179 SER180 VAL181 VAL182 THR183 VAL184 PRO185 SER186 SER187 SER188 LEU189 GLY190 THR191 GLN192 THR193 TYR194 ILE195 CYS196 ASN197 VAL198 ASN199 HIS200 LYS201 PRO202 SER203 ASN204 THR205 LYS206 VAL207 ASP208 LYS209 LYS210 VAL211 GLU212 PRO213 LYS214
Unit 4 MPT1 ASN2 LEU3 HIS4 PHE5 CYS6 GLN7 LEU8 ARG9 CYS10 LYS11 SER12 LEU13 GLY14 LEU15 LEU16 GLY17 LYS18 CYS19 ALA20 GLY21 SER22 PHE23 CYS24 ALA25 CYS26 VLM27
Unit 5 GLU1083 VAL1084 LYS1085 LEU1086 GLU1087 ASN1088 VAL1089 THR1090 GLU1091 ASN1092 PHE1093 ASN1094 MET1095 TRP1096 LYS1097 ASN1098 ASN1099 MET1100 VAL1101 GLU1102 GLN1103 MET1104 HIS1105 GLU1106 ASP1107 ILE1108 ILE1109 SER1110 LEU1111 TRP1112 ASP1113 GLN1114 SER1115 LEU1116 LYS1117 PRO1118 CYS1119 VAL1120 LYS1121 LEU1122 THR1123 PRO1124 LEU1125 CYS1126 VAL1127 GLY1128 ALA1129 GLY1194 SER1195 CYS1196 ASN1197 THR1198 SER1199 VAL1200 ILE1201 THR1202 GLN1203 ALA1204 CYS1205 PRO1206 LYS1207 VAL1208 SER1209 PHE1210 GLU1211 PRO1212 ILE1213 PRO1214 ILE1215 HIS1216 TYR1217 CYS1218 ALA1219 PRO1220 ALA1221 GLY1222 PHE1223 ALA1224 ILE1225 LEU1226 LYS1227 CYS1228 ASN1229 ASP1230 LYS1231 LYS1232 PHE1233 ASN1234 GLY1235 THR1236 GLY1237 PRO1238 CYS1239 THR1240 ASN1241 VAL1242 SER1243 THR1244 VAL1245 GLN1246 CYS1247 THR1248 HIS1249 GLY1250 ILE1251 ARG1252 PRO1253 VAL1254 VAL1255 SER1256 THR1257 GLN1258 LEU1259 LEU1260 LEU1261 ASN1262 GLY1263 SER1264 LEU1265 ALA1266 GLU1267 GLU1268 GLU1269 ILE1270 VAL1271 ILE1272 ARG1273 SER1274 GLU1275 ASN1276 PHE1277 THR1278 ASN1279 ASN1280 ALA1281 LYS1282 THR1283 ILE1284 ILE1285 VAL1286 GLN1287 LEU1288 ASN1289 GLU1290 SER1291 VAL1292 VAL1293 ILE1294 ASN1295 CYS1296 THR1297 GLY1298 ALA1299 GLY1329 HIS1330 CYS1331 ASN1332 LEU1333 SER1334 LYS1335 THR1336 GLN1337 TRP1338 GLU1339 ASN1340 THR1341 LEU1342 GLU1343 GLN1344 ILE1345 ALA1346 ILE1347 LYS1348 LEU1349 LYS1350 GLU1351 GLN1352 PHE1353 GLY1354 ASN1355 ASN1356 LYS1357 THR1358 ILE1359 ILE1360 PHE1361 ASN1362 PRO1363 SER1364 SER1365 GLY1366 GLY1367 ASP1368 PRO1369 GLU1370 ILE1371 VAL1372 THR1373 HIS1374 SER1375 PHE1376 ASN1377 CYS1378 GLY1379 GLY1380 GLU1381 PHE1382 PHE1383 TYR1384 CYS1385 ASN1386 SER1387 THR1388 GLN1389 LEU1390 PHE1391 THR1392 TRP1393 ARG1412 ASN1413 ILE1414 THR1415 LEU1416 PRO1417 CYS1418 ARG1419 ILE1420 LYS1421 GLN1422 ILE1423 ILE1424 ASN1425 MET1426 TRP1427 GLN1428 GLU1429 VAL1430 GLY1431 LYS1432 ALA1433 MET1434 TYR1435 ALA1436 PRO1437 PRO1438 ILE1439 ARG1440 GLY1441 GLN1442 ILE1443 ARG1444 CYS1445 SER1446 SER1447 ASN1448 ILE1449 THR1450 GLY1451 LEU1452 LEU1453 LEU1454 THR1455 ARG1456 ASP1457 GLY1458 GLY1459 LYS1460 ASP1461 THR1462 ASN1463 GLY1464 THR1465 GLU1466 ILE1467 PHE1468 ARG1469 PRO1470 GLY1471 GLY1472 GLY1473 ASP1474 MET1475 ARG1476 ASP1477 ASN1478 TRP1479 ARG1480 SER1481 GLU1482 LEU1483 TYR1484 LYS1485 TYR1486 LYS1487 VAL1488 VAL1489 LYS1490 ILE1491 GLU1492
Unit 6 ASP1001 ILE1002 VAL1003 MET1004 THR1005 GLN1006 SER1007 PRO1008 ALA1009 THR1010 LEU1011 SER1012 VAL1013 SER1014 PRO1015 GLY1016 GLU1017 ARG1018 ALA1019 THR1020 LEU1021 SER1022 CYS1023 ARG1024 ALA1025 SER1026 GLU1027 SER1028 VAL1029 SER1030 SER1031 ASP1032 LEU1033 ALA1034 TRP1035 TYR1036 GLN1037 GLN1038 LYS1039 PRO1040 GLY1041 GLN1042 ALA1043 PRO1044 ARG1045 LEU1046 LEU1047 ILE1048 TYR1049 GLY1050 ALA1051 SER1052 THR1053 ARG1054 ALA1055 THR1056 GLY1057 VAL1058 PRO1059 ALA1060 ARG1061 PHE1062 SER1063 GLY1064 SER1065 GLY1066 SER1067 GLY1068 ALA1069 GLU1070 PHE1071 THR1072 LEU1073 THR1074 ILE1075 SER1076 SER1077 LEU1078 GLN1079 SER1080 GLU1081 ASP1082 PHE1083 ALA1084 VAL1085 TYR1086 TYR1087 CYS1088 GLN1089 GLN1090 TYR1091 ASN1092 ASN1093 TRP1094 PRO1095 PRO1095A ARG1095B TYR1096 THR1097 PHE1098 GLY1099 GLN1100 GLY1101 THR1102 ARG1103 LEU1104 GLU1105 ILE1106 LYS1107 ARG1108 THR1109 VAL1110 ALA1111 ALA1112 PRO1113 SER1114 VAL1115 PHE1116 ILE1117 PHE1118 PRO1119 PRO1120 SER1121 ASP1122 GLU1123 GLN1124 LEU1125 LYS1126 SER1127 GLY1128 THR1129 ALA1130 SER1131 VAL1132 VAL1133 CYS1134 LEU1135 LEU1136 ASN1137 ASN1138 PHE1139 TYR1140 PRO1141 ARG1142 GLU1143 ALA1144 LYS1145 VAL1146 GLN1147 TRP1148 LYS1149 VAL1150 ASP1151 ASN1152 ALA1153 LEU1154 GLN1155 SER1156 GLY1157 ASN1158 SER1159 GLN1160 GLU1161 SER1162 VAL1163 THR1164 GLU1165 GLN1166 ASP1167 SER1168 LYS1169 ASP1170 SER1171 THR1172 TYR1173 SER1174 LEU1175 SER1176 SER1177 THR1178 LEU1179 THR1180 LEU1181 SER1182 LYS1183 ALA1184 ASP1185 TYR1186 GLU1187 LYS1188 HIS1189 LYS1190 VAL1191 TYR1192 ALA1193 CYS1194 GLU1195 VAL1196 THR1197 HIS1198 GLN1199 GLY1200 LEU1201 SER1202 SER1203 PRO1204 VAL1205 THR1206 LYS1207 SER1208 PHE1209 ASN1210 ARG1211 GLY1212
Unit 7 GLU1001 VAL1002 GLN1003 LEU1004 VAL1005 GLU1006 SER1007 GLY1008 ALA1009 GLU1010 VAL1011 LYS1012 LYS1013 PRO1014 GLY1015 SER1016 SER1017 VAL1018 LYS1019 VAL1020 SER1021 CYS1022 LYS1023 ALA1024 SER1025 GLY1026 ASP1027 THR1028 PHE1029 ILE1030 ARG1031 TYR1032 SER1033 PHE1034 THR1035 TRP1036 VAL1037 ARG1038 GLN1039 ALA1040 PRO1041 GLY1042 GLN1043 GLY1044 LEU1045 GLU1046 TRP1047 MET1048 GLY1049 ARG1050 ILE1051 ILE1052 THR1052A ILE1053 LEU1054 ASP1055 VAL1056 ALA1057 HIS1058 TYR1059 ALA1060 PRO1061 HIS1062 LEU1063 GLN1064 GLY1065 ARG1066 VAL1067 THR1068 ILE1069 THR1070 ALA1071 ASP1072 LYS1073 SER1074 THR1075 SER1076 THR1077 VAL1078 TYR1079 LEU1080 GLU1081 LEU1082 ARG1082A ASN1082B LEU1082C ARG1083 SER1084 ASP1085 ASP1086 THR1087 ALA1088 VAL1089 TYR1090 PHE1091 CYS1092 ALA1093 GLY1094 VAL1095 TYR1096 GLU1097 GLY1098 GLU1099 ALA1100 ASP1100A GLU1100B GLY1100C GLU1100D TYR1100E ASP1100F ASN1100G ASN1100H GLY1100I PHE1100J LEU1100K LYS1101 HIS1102 TRP1103 GLY1104 GLN1105 GLY1106 THR1107 LEU1108 VAL1109 THR1110 VAL1111 SER1112 SER1113 ALA1114 SER1115 THR1116 LYS1117 GLY1118 PRO1119 SER1120 VAL1121 PHE1122 PRO1123 LEU1124 ALA1125 PRO1126 SER1127 SER1128 LYS1129 SER1130 THR1131 SER1132 GLY1133 GLY1134 THR1135 ALA1136 ALA1137 LEU1138 GLY1139 CYS1140 LEU1141 VAL1142 LYS1143 ASP1144 TYR1145 PHE1146 PRO1147 GLU1148 PRO1149 VAL1150 THR1151 VAL1152 SER1153 TRP1154 ASN1155 SER1156 GLY1157 ALA1158 LEU1159 THR1160 SER1161 GLY1162 VAL1163 HIS1164 THR1165 PHE1166 PRO1167 ALA1168 VAL1169 LEU1170 GLN1171 SER1172 SER1173 GLY1174 LEU1175 TYR1176 SER1177 LEU1178 SER1179 SER1180 VAL1181 VAL1182 THR1183 VAL1184 PRO1185 SER1186 SER1187 SER1188 LEU1189 GLY1190 THR1191 GLN1192 THR1193 TYR1194 ILE1195 CYS1196 ASN1197 VAL1198 ASN1199 HIS1200 LYS1201 PRO1202 SER1203 ASN1204 THR1205 LYS1206 VAL1207 ASP1208 LYS1209 LYS1210 VAL1211 GLU1212 PRO1213 LYS1214
Unit 8 MPT1001 ASN1002 LEU1003 HIS1004 PHE1005 CYS1006 GLN1007 LEU1008 ARG1009 CYS1010 LYS1011 SER1012 LEU1013 GLY1014 LEU1015 LEU1016 GLY1017 LYS1018 CYS1019 ALA1020 GLY1021 SER1022 PHE1023 CYS1024 ALA1025 CYS1026 VLM1027

Ligands
Unit 9 NAG588 NAG734 NAG741 NAG762 NAG776 NAG789 NAG795 NAG886 IPA901 EDO903
Unit 10 EDO904
Unit 11 IPA902 NAG1588 NAG1734 NAG1741 NAG1762 NAG1776 NAG1789 NAG1795 NAG1886

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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany