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Sequence, Chains, Asymmetric and Biological Units

Title CRYSTAL STRUCTURE OF HUMAN AUTOREACTIVE-VALPHA24 NKT TCR IN WITH CD1D-BETA-GALACTOSYLCERAMIDE
Keywords CD1D, AUTOIMMUNITY, SELF-RECOGNITION, NKT, EXTRACELLULAR, IM SYSTEM
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   3SDX     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   ANTIGEN-PRESENTING GLYCOPROTEIN CD1D  A 275 2184 0
2  Protein   BETA-2-MICROGLOBULIN  B 97 783 0
3  Protein   NKT TCR VALPHA24 CHAIN  E 196 1485 0
4  Protein   NKT TCR AUTOREACTIVE-VBETA11 CHAIN  F 242 1915 0
5  Protein   NKT TCR VALPHA24 CHAIN  G 196 1507 0
6  Protein   ANTIGEN-PRESENTING GLYCOPROTEIN CD1D  C 268 2135 0
7  Protein   BETA-2-MICROGLOBULIN  D 97 789 0
8  Protein   NKT TCR AUTOREACTIVE-VBETA11 CHAIN  H 240 1870 0
9  Ligand   ANTIGEN-PRESENTING GLYCOPROTEIN CD1D  A 1 0 45
10  Ligand   ANTIGEN-PRESENTING GLYCOPROTEIN CD1D  C 1 0 45
11 Water     66 0 66
total       1679 12668 156
Proteins
Unit 1 ARG6 LEU7 PHE8 PRO9 LEU10 ARG11 CYS12 LEU13 GLN14 ILE15 SER16 SER17 PHE18 ALA19 ASN20 SER21 SER22 TRP23 THR24 ARG25 THR26 ASP27 GLY28 LEU29 ALA30 TRP31 LEU32 GLY33 GLU34 LEU35 GLN36 THR37 HIS38 SER39 TRP40 SER41 ASN42 ASP43 SER44 ASP45 THR46 VAL47 ARG48 SER49 LEU50 LYS51 PRO52 TRP53 SER54 GLN55 GLY56 THR57 PHE58 SER59 ASP60 GLN61 GLN62 TRP63 GLU64 THR65 LEU66 GLN67 HIS68 ILE69 PHE70 ARG71 VAL72 TYR73 ARG74 SER75 SER76 PHE77 THR78 ARG79 ASP80 VAL81 LYS82 GLU83 PHE84 ALA85 LYS86 MET87 LEU88 ARG89 LEU90 SER91 TYR92 PRO93 LEU94 GLU95 LEU96 GLN97 VAL98 SER99 ALA100 GLY101 CYS102 GLU103 VAL104 HIS105 PRO106 GLY107 ASN108 ALA109 SER110 ASN111 ASN112 PHE113 PHE114 HIS115 VAL116 ALA117 PHE118 GLN119 GLY120 LYS121 ASP122 ILE123 LEU124 SER125 PHE126 GLN127 GLY128 THR129 SER130 TRP131 GLU132 PRO133 THR134 GLN135 GLU136 ALA137 PRO138 LEU139 TRP140 VAL141 ASN142 LEU143 ALA144 ILE145 GLN146 VAL147 LEU148 ASN149 GLN150 ASP151 LYS152 TRP153 THR154 ARG155 GLU156 THR157 VAL158 GLN159 TRP160 LEU161 LEU162 ASN163 GLY164 THR165 CYS166 PRO167 GLN168 PHE169 VAL170 SER171 GLY172 LEU173 LEU174 GLU175 SER176 GLY177 LYS178 SER179 GLU180 LEU181 LYS182 LYS183 GLN184 VAL185 LYS186 PRO187 LYS188 ALA189 TRP190 LEU191 SER192 ARG193 GLY194 PRO195 SER196 PRO197 GLY198 PRO199 GLY200 ARG201 LEU202 LEU203 LEU204 VAL205 CYS206 HIS207 VAL208 SER209 GLY210 PHE211 TYR212 PRO213 LYS214 PRO215 VAL216 TRP217 VAL218 LYS219 TRP220 MET221 ARG222 GLY223 GLU224 GLN225 GLU226 GLN227 GLN228 GLY229 THR230 GLN231 PRO232 GLY233 ASP234 ILE235 LEU236 PRO237 ASN238 ALA239 ASP240 GLU241 THR242 TRP243 TYR244 LEU245 ARG246 ALA247 THR248 LEU249 ASP250 VAL251 VAL252 ALA253 GLY254 GLU255 ALA256 ALA257 GLY258 LEU259 SER260 CYS261 ARG262 VAL263 LYS264 HIS265 SER266 SER267 LEU268 GLU269 GLY270 GLN271 ASP272 ILE273 VAL274 LEU275 TYR276 TRP277 HIS278 HIS279 HIS280
Unit 2 ILE1 GLN2 ARG3 THR4 PRO5 LYS6 ILE7 GLN8 VAL9 TYR10 SER11 ARG12 HIS13 PRO14 ALA15 GLU16 ASN17 GLY18 LYS19 SER20 ASN21 PHE22 LEU23 ASN24 CYS25 TYR26 VAL27 SER28 GLY29 PHE30 HIS31 PRO32 SER33 ASP34 ILE35 GLU36 VAL37 ASP38 LEU39 LEU40 LYS41 ASN42 GLY43 GLU44 ARG45 ILE46 GLU47 LYS48 VAL49 GLU50 HIS51 SER52 ASP53 LEU54 SER55 PHE56 SER57 LYS58 ASP59 TRP60 SER61 PHE62 TYR63 LEU64 LEU65 TYR66 TYR67 THR68 GLU69 PHE70 THR71 PRO72 THR73 GLU74 LYS75 ASP76 GLU77 TYR78 ALA79 CYS80 ARG81 VAL82 ASN83 HIS84 VAL85 THR86 LEU87 SER88 GLN89 PRO90 LYS91 ILE92 VAL93 LYS94 TRP95 ASP96 ARG97
Unit 3 ASN1 GLN2 VAL3 GLU4 GLN5 SER6 PRO7 GLN8 SER9 LEU10 ILE11 ILE12 LEU13 GLU14 GLY15 LYS16 ASN17 CYS18 THR19 LEU20 GLN21 CYS22 ASN23 TYR24 THR25 VAL26 SER27 PRO28 PHE29 SER30 ASN31 LEU32 ARG33 TRP34 TYR35 LYS36 GLN37 ASP38 THR39 GLY40 ARG41 GLY42 PRO43 VAL44 SER45 LEU46 THR47 ILE48 MET49 THR50 PHE51 SER52 GLU53 ASN54 THR55 LYS56 SER57 ASN58 GLY59 ARG60 TYR61 THR62 ALA63 THR64 LEU65 ASP66 ALA67 ASP68 THR69 LYS70 GLN71 SER72 SER73 LEU74 HIS75 ILE76 THR77 ALA78 SER79 GLN80 LEU81 SER82 ASP83 SER84 ALA85 SER86 TYR87 ILE88 CYS89 VAL90 VAL91 SER92 ASP93 ARG94 GLY95 SER96 THR97 LEU98 GLY99 ARG100 LEU101 TYR102 PHE103 GLY104 ARG105 GLY106 THR107 GLN108 LEU109 THR110 VAL111 TRP112 PRO113 ASP114 ILE115 GLN116 ASN117 PRO118 ASP119 PRO120 ALA121 VAL122 TYR123 GLN124 LEU125 ARG126 ASP127 SER128 SER134 VAL135 CYS136 LEU137 PHE138 THR139 ASP140 PHE141 ASP142 SER143 GLN144 THR145 ASN146 VAL147 SER148 GLN149 SER150 SER153 ASP154 VAL155 TYR156 ILE157 THR158 ASP159 LYS160 CYS161 VAL162 LEU163 ASP164 MET165 ARG166 SER167 MET168 ASP169 PHE170 LYS171 SER172 ASN173 SER174 ALA175 VAL176 ALA177 TRP178 SER179 ASN180 LYS181 SER182 ASP183 PHE184 ALA185 CYS186 ALA187 ASN188 ALA189 PHE190 ASN191 ASN192 SER193 ILE194 ILE195 PRO196 GLU197 ASP198 THR199 PHE200 PHE201 PRO202 SER203
Unit 4 ALA2 ASP3 ILE4 TYR5 GLN6 THR7 PRO8 ARG9 TYR10 LEU11 VAL12 ILE13 GLY14 THR15 GLY16 LYS17 LYS18 ILE19 THR20 LEU21 GLU22 CYS23 SER24 GLN25 THR26 MET27 GLY28 HIS29 ASP30 LYS31 MET32 TYR33 TRP34 TYR35 GLN36 GLN37 ASP38 PRO39 GLY40 MET41 GLU42 LEU43 HIS44 LEU45 ILE46 HIS47 TYR48 SER49 TYR50 GLY51 VAL52 ASN53 SER54 THR55 GLU56 LYS57 GLY58 ASP59 LEU60 SER61 SER62 GLU63 SER64 THR65 VAL66 SER67 ARG68 ILE69 ARG70 THR71 GLU72 HIS73 PHE74 PRO75 LEU76 THR77 LEU78 GLU79 SER80 ALA81 ARG82 PRO83 SER84 HIS85 THR86 SER87 GLN88 TYR89 LEU90 CYS91 ALA92 SER93 SER94 GLU95 PHE96 GLY97 THR102 GLN103 GLU104 THR105 GLN106 TYR107 PHE108 GLY109 PRO110 GLY111 THR112 ARG113 LEU114 LEU115 VAL116 LEU117 GLU118 ASP119 LEU120 LYS121 ASN122 VAL123 PHE124 PRO125 PRO126 GLU127 VAL128 ALA129 VAL130 PHE131 GLU132 PRO133 SER134 GLU135 ALA136 GLU137 ILE138 SER139 HIS140 THR141 GLN142 LYS143 ALA144 THR145 LEU146 VAL147 CYS148 LEU149 ALA150 THR151 GLY152 PHE153 TYR154 PRO155 ASP156 HIS157 VAL158 GLU159 LEU160 SER161 TRP162 TRP163 VAL164 ASN165 GLY166 LYS167 GLU168 VAL169 HIS170 SER171 GLY172 VAL173 CYS174 THR175 ASP176 PRO177 GLN178 PRO179 LEU180 LYS181 GLU182 GLN183 PRO184 ALA185 LEU186 ASN187 ASP188 SER189 ARG190 TYR191 ALA192 LEU193 SER194 SER195 ARG196 LEU197 ARG198 VAL199 SER200 ALA201 THR202 PHE203 TRP204 GLN205 ASN206 PRO207 ARG208 ASN209 HIS210 PHE211 ARG212 CYS213 GLN214 VAL215 GLN216 PHE217 TYR218 GLY219 LEU220 SER221 GLU222 ASN223 ASP224 GLU225 TRP226 THR227 GLN228 ASP229 ARG230 ALA231 LYS232 PRO233 VAL234 THR235 GLN236 ILE237 VAL238 SER239 ALA240 GLU241 ALA242 TRP243 GLY244 ARG245 ALA246 ASP247
Unit 5 ASN1 GLN2 VAL3 GLU4 GLN5 SER6 PRO7 GLN8 SER9 LEU10 ILE11 ILE12 LEU13 GLU14 GLY15 LYS16 ASN17 CYS18 THR19 LEU20 GLN21 CYS22 ASN23 TYR24 THR25 VAL26 SER27 PRO28 PHE29 SER30 ASN31 LEU32 ARG33 TRP34 TYR35 LYS36 GLN37 ASP38 THR39 GLY40 ARG41 GLY42 PRO43 VAL44 SER45 LEU46 THR47 ILE48 MET49 THR50 PHE51 SER52 GLU53 ASN54 THR55 LYS56 SER57 ASN58 GLY59 ARG60 TYR61 THR62 ALA63 THR64 LEU65 ASP66 ALA67 ASP68 THR69 LYS70 GLN71 SER72 SER73 LEU74 HIS75 ILE76 THR77 ALA78 SER79 GLN80 LEU81 SER82 ASP83 SER84 ALA85 SER86 TYR87 ILE88 CYS89 VAL90 VAL91 SER92 ASP93 ARG94 GLY95 SER96 THR97 LEU98 GLY99 ARG100 LEU101 TYR102 PHE103 GLY104 ARG105 GLY106 THR107 GLN108 LEU109 THR110 VAL111 TRP112 PRO113 ASP114 ILE115 GLN116 ASN117 PRO118 ASP119 PRO120 ALA121 VAL122 TYR123 GLN124 LEU125 ARG126 ASP127 SER128 SER134 VAL135 CYS136 LEU137 PHE138 THR139 ASP140 PHE141 ASP142 SER143 GLN144 THR145 ASN146 VAL147 SER148 GLN149 SER150 SER153 ASP154 VAL155 TYR156 ILE157 THR158 ASP159 LYS160 CYS161 VAL162 LEU163 ASP164 MET165 ARG166 SER167 MET168 ASP169 PHE170 LYS171 SER172 ASN173 SER174 ALA175 VAL176 ALA177 TRP178 SER179 ASN180 LYS181 SER182 ASP183 PHE184 ALA185 CYS186 ALA187 ASN188 ALA189 PHE190 ASN191 ASN192 SER193 ILE194 ILE195 PRO196 GLU197 ASP198 THR199 PHE200 PHE201 PRO202 SER203
Unit 6 ARG6 LEU7 PHE8 PRO9 LEU10 ARG11 CYS12 LEU13 GLN14 ILE15 SER16 SER17 PHE18 ALA19 ASN20 SER21 SER22 TRP23 THR24 ARG25 THR26 ASP27 GLY28 LEU29 ALA30 TRP31 LEU32 GLY33 GLU34 LEU35 GLN36 THR37 HIS38 SER39 TRP40 SER41 ASN42 ASP43 SER44 ASP45 THR46 VAL47 ARG48 SER49 LEU50 LYS51 PRO52 TRP53 SER54 GLN55 GLY56 THR57 PHE58 SER59 ASP60 GLN61 GLN62 TRP63 GLU64 THR65 LEU66 GLN67 HIS68 ILE69 PHE70 ARG71 VAL72 TYR73 ARG74 SER75 SER76 PHE77 THR78 ARG79 ASP80 VAL81 LYS82 GLU83 PHE84 ALA85 LYS86 MET87 LEU88 ARG89 LEU90 SER91 TYR92 PRO93 LEU94 GLU95 LEU96 GLN97 VAL98 SER99 ALA100 GLY101 CYS102 GLU103 VAL104 HIS105 PRO106 GLY107 ASN108 ALA109 SER110 ASN111 ASN112 PHE113 PHE114 HIS115 VAL116 ALA117 PHE118 GLN119 GLY120 LYS121 ASP122 ILE123 LEU124 SER125 PHE126 GLN127 GLY128 THR129 SER130 TRP131 GLU132 PRO133 THR134 GLN135 GLU136 ALA137 PRO138 LEU139 TRP140 VAL141 ASN142 LEU143 ALA144 ILE145 GLN146 VAL147 LEU148 ASN149 GLN150 ASP151 LYS152 TRP153 THR154 ARG155 GLU156 THR157 VAL158 GLN159 TRP160 LEU161 LEU162 ASN163 GLY164 THR165 CYS166 PRO167 GLN168 PHE169 VAL170 SER171 GLY172 LEU173 LEU174 GLU175 SER176 GLY177 LYS178 SER179 GLU180 LEU181 LYS182 LYS183 GLN184 VAL185 LYS186 PRO187 LYS188 ALA189 TRP190 LEU191 SER192 ARG193 GLY194 PRO195 SER196 PRO197 GLY198 PRO199 GLY200 ARG201 LEU202 LEU203 LEU204 VAL205 CYS206 HIS207 VAL208 SER209 GLY210 PHE211 TYR212 PRO213 LYS214 PRO215 VAL216 TRP217 VAL218 LYS219 TRP220 MET221 ARG222 GLY223 GLU224 GLN225 GLU226 GLN227 GLN228 GLY229 THR230 GLN231 PRO232 GLY233 ASP234 ILE235 LEU236 PRO237 ASN238 ALA239 ASP240 GLU241 THR242 TRP243 TYR244 LEU245 ARG246 ALA247 THR248 LEU249 ASP250 VAL251 VAL252 ALA253 GLY254 GLU255 SER260 CYS261 ARG262 VAL263 LYS264 HIS265 SER266 SER267 LEU268 GLU269 GLY270 GLN271 ASP272 ILE273 VAL274 LEU275 TYR276 TRP277
Unit 7 ILE1 GLN2 ARG3 THR4 PRO5 LYS6 ILE7 GLN8 VAL9 TYR10 SER11 ARG12 HIS13 PRO14 ALA15 GLU16 ASN17 GLY18 LYS19 SER20 ASN21 PHE22 LEU23 ASN24 CYS25 TYR26 VAL27 SER28 GLY29 PHE30 HIS31 PRO32 SER33 ASP34 ILE35 GLU36 VAL37 ASP38 LEU39 LEU40 LYS41 ASN42 GLY43 GLU44 ARG45 ILE46 GLU47 LYS48 VAL49 GLU50 HIS51 SER52 ASP53 LEU54 SER55 PHE56 SER57 LYS58 ASP59 TRP60 SER61 PHE62 TYR63 LEU64 LEU65 TYR66 TYR67 THR68 GLU69 PHE70 THR71 PRO72 THR73 GLU74 LYS75 ASP76 GLU77 TYR78 ALA79 CYS80 ARG81 VAL82 ASN83 HIS84 VAL85 THR86 LEU87 SER88 GLN89 PRO90 LYS91 ILE92 VAL93 LYS94 TRP95 ASP96 ARG97
Unit 8 GLU1 ALA2 ASP3 ILE4 TYR5 GLN6 THR7 PRO8 ARG9 TYR10 LEU11 VAL12 ILE13 GLY14 THR15 GLY16 LYS17 LYS18 ILE19 THR20 LEU21 GLU22 CYS23 SER24 GLN25 THR26 MET27 GLY28 HIS29 ASP30 LYS31 MET32 TYR33 TRP34 TYR35 GLN36 GLN37 ASP38 PRO39 GLY40 MET41 GLU42 LEU43 HIS44 LEU45 ILE46 HIS47 TYR48 SER49 TYR50 GLY51 VAL52 ASN53 SER54 THR55 GLU56 LYS57 GLY58 SER61 SER62 GLU63 SER64 THR65 VAL66 SER67 ARG68 ILE69 ARG70 THR71 GLU72 HIS73 PHE74 PRO75 LEU76 THR77 LEU78 GLU79 SER80 ALA81 ARG82 PRO83 SER84 HIS85 THR86 SER87 GLN88 TYR89 LEU90 CYS91 ALA92 SER93 SER94 GLU95 PHE96 THR102 GLN103 GLU104 THR105 GLN106 TYR107 PHE108 GLY109 PRO110 GLY111 THR112 ARG113 LEU114 LEU115 VAL116 LEU117 GLU118 ASP119 LEU120 LYS121 ASN122 VAL123 PHE124 PRO125 PRO126 GLU127 VAL128 ALA129 VAL130 PHE131 GLU132 PRO133 SER134 GLU135 ALA136 GLU137 ILE138 SER139 HIS140 THR141 GLN142 LYS143 ALA144 THR145 LEU146 VAL147 CYS148 LEU149 ALA150 THR151 GLY152 PHE153 TYR154 PRO155 ASP156 HIS157 VAL158 GLU159 LEU160 SER161 TRP162 TRP163 VAL164 ASN165 GLY166 LYS167 GLU168 VAL169 HIS170 SER171 GLY172 VAL173 CYS174 THR175 ASP176 PRO177 GLN178 PRO179 LEU180 LYS181 GLU182 GLN183 PRO184 ALA185 LEU186 ASN187 ASP188 SER189 ARG190 TYR191 ALA192 LEU193 SER194 SER195 ARG196 LEU197 ARG198 VAL199 SER200 ALA201 THR202 PHE203 TRP204 GLN205 ASN206 PRO207 ARG208 ASN209 HIS210 PHE211 ARG212 CYS213 GLN214 VAL215 GLN216 PHE217 TYR218 GLY219 LEU220 SER221 GLU222 ASN223 ASP224 GLU225 TRP226 THR227 GLN228 ASP229 ARG230 ALA231 LYS232 PRO233 VAL234 THR235 GLN236 ILE237 VAL238 SER239 ALA240 GLU241 ALA242 TRP243 GLY244 ARG245 ALA246 ASP247
Ligands
Unit 9 GCY601
Unit 10 GCY602
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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany