3SDA - Sequence, Chains, Asymmetric and Biological Units

• Title: CRYSTAL STRUCTURE OF AUTOREACTIVE-VALPHA14-VBETA6 NKT TCR IN WITH CD1D-BETA-GALACTOSYLCERAMIDE
• Keywords: CD1D, BETA-LINKED ANTIGEN, IMMUNITY, NKT, AUTOREACTIVE, IMMU
• Experiment: X-ray diffraction
• Number of Models: 1

Database	ID code	Status	Coordinate files
			Header	Asymmetric unit	Biological unit
PDB	3SDA	released	available	available	Quaternary Structure Server

Asymmetric unit from PDB

Unit	Type	Name	Chain ID	Residues	Atoms	Hetatoms
1	Protein	ANTIGEN-PRESENTING GLYCOPROTEIN CD1D1	A	290	2333	0
2	Protein	BETA-2-MICROGLOBULIN	B	99	814	0
3	Protein	NKT TCR VALPHA14 CHAIN	C	196	1511	0
4	Protein	NKT TCR AUTOREACTIVE-VBETA6 CHAIN	D	239	1900	0
5	Ligand		E	2	0	28
6	Ligand	ANTIGEN-PRESENTING GLYCOPROTEIN CD1D1	A	3	0	85
7	Ligand	BETA-2-MICROGLOBULIN	B	1	0	6
8	Water			62	0	62
total				892	6558	181

Proteins

Unit 1	LYS 6 ASN 7 TYR 8 THR 9 PHE 10 ARG 11 CYS 12 LEU 13 GLN 14 MET 15 SER 16 SER 17 PHE 18 ALA 19 ASN 20 ARG 21 SER 22 TRP 23 SER 24 ARG 25 THR 26 ASP 27 SER 28 VAL 29 VAL 30 TRP 31 LEU 32 GLY 33 ASP 34 LEU 35 GLN 36 THR 37 HIS 38 ARG 39 TRP 40 SER 41 ASN 42 ASP 43 SER 44 ALA 45 THR 46 ILE 47 SER 48 PHE 49 THR 50 LYS 51 PRO 52 TRP 53 SER 54 GLN 55 GLY 56 LYS 57 LEU 58 SER 59 ASN 60 GLN 61 GLN 62 TRP 63 GLU 64 LYS 65 LEU 66 GLN 67 HIS 68 MET 69 PHE 70 GLN 71 VAL 72 TYR 73 ARG 74 VAL 75 SER 76 PHE 77 THR 78 ARG 79 ASP 80 ILE 81 GLN 82 GLU 83 LEU 84 VAL 85 LYS 86 MET 87 MET 88 SER 89 PRO 90 LYS 91 GLU 92 ASP 93 TYR 94 PRO 95 ILE 96 GLU 97 ILE 98 GLN 99 LEU 100 SER 101 ALA 102 GLY 103 CYS 104 GLU 105 MET 106 TYR 107 PRO 108 GLY 109 ASN 110 ALA 111 SER 112 GLU 113 SER 114 PHE 115 LEU 116 HIS 117 VAL 118 ALA 119 PHE 120 GLN 121 GLY 122 LYS 123 TYR 124 VAL 125 VAL 126 ARG 127 PHE 128 TRP 129 GLY 130 THR 131 SER 132 TRP 133 GLN 134 THR 135 VAL 136 PRO 137 GLY 138 ALA 139 PRO 140 SER 141 TRP 142 LEU 143 ASP 144 LEU 145 PRO 146 ILE 147 LYS 148 VAL 149 LEU 150 ASN 151 ALA 152 ASP 153 GLN 154 GLY 155 THR 156 SER 157 ALA 158 THR 159 VAL 160 GLN 161 MET 162 LEU 163 LEU 164 ASN 165 ASP 166 THR 167 CYS 168 PRO 169 LEU 170 PHE 171 VAL 172 ARG 173 GLY 174 LEU 175 LEU 176 GLU 177 ALA 178 GLY 179 LYS 180 SER 181 ASP 182 LEU 183 GLU 184 LYS 185 GLN 186 GLU 187 LYS 188 PRO 189 VAL 190 ALA 191 TRP 192 LEU 193 SER 194 SER 195 VAL 196 PRO 197 SER 198 SER 199 ALA 200 HIS 201 GLY 202 HIS 203 ARG 204 GLN 205 LEU 206 VAL 207 CYS 208 HIS 209 VAL 210 SER 211 GLY 212 PHE 213 TYR 214 PRO 215 LYS 216 PRO 217 VAL 218 TRP 219 VAL 220 MET 221 TRP 222 MET 223 ARG 224 GLY 225 ASP 226 GLN 227 GLU 228 GLN 229 GLN 230 GLY 231 THR 232 HIS 233 ARG 234 GLY 235 ASP 236 PHE 237 LEU 238 PRO 239 ASN 240 ALA 241 ASP 242 GLU 243 THR 244 TRP 245 TYR 246 LEU 247 GLN 248 ALA 249 THR 250 LEU 251 ASP 252 VAL 253 GLU 254 ALA 255 GLY 256 GLU 257 GLU 258 ALA 259 GLY 260 LEU 261 ALA 262 CYS 263 ARG 264 VAL 265 LYS 266 HIS 267 SER 268 SER 269 LEU 270 GLY 271 GLY 272 GLN 273 ASP 274 ILE 275 ILE 276 LEU 277 TYR 278 TRP 279 GLY 280 SER 281 LEU 282 HIS 283 HIS 284 ILE 285 LEU 286 ASP 287 ALA 288 GLN 289 LYS 290 MET 291 VAL 292 TRP 293 ASN 294 HIS 295
Unit 2	ILE 1 GLN 2 LYS 3 THR 4 PRO 5 GLN 6 ILE 7 GLN 8 VAL 9 TYR 10 SER 11 ARG 12 HIS 13 PRO 14 PRO 15 GLU 16 ASN 17 GLY 18 LYS 19 PRO 20 ASN 21 ILE 22 LEU 23 ASN 24 CYS 25 TYR 26 VAL 27 THR 28 GLN 29 PHE 30 HIS 31 PRO 32 PRO 33 HIS 34 ILE 35 GLU 36 ILE 37 GLN 38 MET 39 LEU 40 LYS 41 ASN 42 GLY 43 LYS 44 LYS 45 ILE 46 PRO 47 LYS 48 VAL 49 GLU 50 MET 51 SER 52 ASP 53 MET 54 SER 55 PHE 56 SER 57 LYS 58 ASP 59 TRP 60 SER 61 PHE 62 TYR 63 ILE 64 LEU 65 ALA 66 HIS 67 THR 68 GLU 69 PHE 70 THR 71 PRO 72 THR 73 GLU 74 THR 75 ASP 76 THR 77 TYR 78 ALA 79 CYS 80 ARG 81 VAL 82 LYS 83 HIS 84 ALA 85 SER 86 MET 87 ALA 88 GLU 89 PRO 90 LYS 91 THR 92 VAL 93 TYR 94 TRP 95 ASP 96 ARG 97 ASP 98 MET 99
Unit 3	THR 1 GLN 2 VAL 3 GLU 4 GLN 5 SER 6 PRO 7 GLN 8 SER 9 LEU 10 VAL 11 VAL 12 ARG 13 GLN 14 GLY 15 GLU 16 ASN 17 SER 18 VAL 19 LEU 20 GLN 21 CYS 22 ASN 23 TYR 24 SER 25 VAL 26 THR 27 PRO 28 ASP 29 ASN 30 HIS 31 LEU 32 ARG 33 TRP 34 PHE 35 LYS 36 GLN 37 ASP 38 THR 39 GLY 40 LYS 41 GLY 42 LEU 43 VAL 44 SER 45 LEU 46 THR 47 VAL 48 LEU 49 VAL 50 ASP 51 GLN 52 LYS 53 ASP 54 LYS 55 THR 56 SER 57 ASN 58 GLY 59 ARG 60 TYR 62 SER 63 ALA 64 THR 65 LEU 66 ASP 67 LYS 68 ASP 69 ALA 70 LYS 71 HIS 72 SER 73 THR 74 LEU 75 HIS 76 ILE 77 THR 78 ALA 79 THR 80 LEU 81 LEU 82 ASP 83 ASP 84 THR 85 ALA 86 THR 87 TYR 88 ILE 89 CYS 90 VAL 91 VAL 92 GLY 93 ASP 94 ARG 95 GLY 96 SER 97 ALA 98 LEU 99 GLY 100 ARG 103 LEU 104 HIS 105 PHE 106 GLY 107 ALA 108 GLY 109 THR 110 GLN 111 LEU 112 ILE 113 VAL 114 ILE 115 PRO 116 ASP 117 ILE 118 GLN 119 ASN 120 PRO 121 ASP 122 PRO 123 ALA 124 VAL 125 TYR 126 GLN 127 LEU 128 ARG 129 ASP 130 SER 131 LYS 132 SER 133 SER 134 ASP 135 LYS 136 SER 137 VAL 138 CYS 139 LEU 140 PHE 141 THR 142 ASP 143 PHE 144 ASP 145 SER 146 GLN 147 THR 148 ASN 149 VAL 150 SER 151 GLN 152 SER 153 LYS 154 ASP 155 SER 156 ASP 157 VAL 158 TYR 159 ILE 160 THR 161 ASP 162 LYS 163 CYS 164 VAL 165 LEU 166 ASP 167 MET 168 ARG 169 SER 170 MET 171 ASP 172 PHE 173 LYS 174 SER 175 ASN 176 SER 177 ALA 178 VAL 179 ALA 180 TRP 181 SER 182 ALA 188 CYS 189 ALA 190 ASN 191 ALA 192 PHE 193 ASN 194 ASN 195 SER 196 ILE 197 ILE 198 PRO 199 GLU 200 ASP 201 THR 202 PHE 203 PHE 204
Unit 4	GLY 1 GLY 2 ILE 3 ILE 4 THR 5 GLN 6 THR 7 PRO 8 LYS 9 PHE 10 LEU 11 ILE 12 GLY 13 GLN 14 GLU 15 GLY 16 GLN 17 LYS 18 LEU 19 THR 20 LEU 21 LYS 22 CYS 23 GLN 24 GLN 25 ASN 26 PHE 27 ASN 28 HIS 29 ASP 30 THR 31 MET 32 TYR 33 TRP 34 TYR 35 ARG 36 GLN 37 ASP 38 SER 39 GLY 40 LYS 41 GLY 42 LEU 43 ARG 44 LEU 45 ILE 46 TYR 47 TYR 48 SER 49 TYR 50 GLY 51 ALA 52 GLY 53 SER 54 THR 55 GLU 56 LYS 57 GLY 58 ASP 59 LEU 60 SER 61 GLU 62 GLY 63 TYR 64 ASP 65 ALA 66 SER 67 ARG 68 GLU 69 LYS 70 LYS 71 SER 72 SER 73 PHE 74 SER 75 LEU 76 THR 77 VAL 78 THR 79 SER 80 ALA 81 GLN 82 LYS 83 ASN 84 GLU 85 MET 86 ALA 87 VAL 88 PHE 89 LEU 90 CYS 91 ALA 92 SER 93 GLY 94 SER 95 LEU 96 LEU 97 ASP 98 VAL 99 ARG 100 GLU 105 VAL 106 PHE 107 PHE 108 GLY 109 LYS 110 GLY 111 THR 112 ARG 113 LEU 114 THR 115 VAL 116 VAL 117 GLU 118 ASP 119 LEU 120 LYS 121 ASN 122 VAL 123 PHE 124 PRO 125 PRO 126 GLU 127 VAL 128 ALA 129 VAL 130 PHE 131 GLU 132 PRO 133 SER 134 GLU 135 ALA 136 GLU 137 ILE 138 SER 139 HIS 140 THR 141 GLN 142 LYS 143 ALA 144 THR 145 LEU 146 VAL 147 CYS 148 LEU 149 ALA 150 THR 151 GLY 152 PHE 153 TYR 154 PRO 155 ASP 156 HIS 157 VAL 158 GLU 159 LEU 160 SER 161 TRP 162 TRP 163 VAL 164 ASN 165 GLY 166 LYS 167 GLU 168 VAL 169 HIS 170 SER 171 GLY 172 VAL 173 CYS 174 THR 175 ASP 176 PRO 177 GLN 178 PRO 179 LEU 180 LYS 181 GLU 182 GLN 183 PRO 184 ALA 185 LEU 186 ASN 187 ASP 188 SER 189 ARG 190 TYR 191 ALA 192 LEU 193 SER 194 SER 195 ARG 196 LEU 197 ARG 198 VAL 199 SER 200 ALA 201 THR 202 PHE 203 TRP 204 GLN 205 ASN 206 PRO 207 ARG 208 ASN 209 HIS 210 PHE 211 ARG 212 CYS 213 GLN 214 VAL 215 GLN 216 PHE 217 TYR 218 GLY 219 LEU 220 SER 221 GLU 222 ASN 223 ASP 224 GLU 225 TRP 226 THR 227 GLN 228 ASP 229 ARG 230 ALA 231 LYS 232 PRO 233 VAL 234 THR 235 GLN 236 ILE 237 VAL 238 SER 239 ALA 240 GLU 241 ALA 242 TRP 243

Ligands

Unit 5	NAG 1 NAG 2
Unit 6	NAG 303 NAG 304 GCY 601
Unit 7	GOL 100