6MIY
Crystal structure of the mCD1d/xxa (JJ239)/iNKTCR ternary complex
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, F (C, G) | T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN | polymer | 209 | 23055.6 | 2 | UniProt (A0A0B4J1J9) UniProt (K7N5M3) Pfam (PF07686) Pfam (PF09291) | Mus musculus (Mouse) | T cell receptor alpha variable 11D,Human nkt tcr beta chain |
| 2 | B, G (D, H) | Beta-chain,T cell receptor chain,T cell receptor beta constant 2, CHIMERIC PROTEIN | polymer | 241 | 27027.0 | 2 | UniProt (A2NTY6) UniProt (A0N8J3) UniProt (A0A5B9) Pfam (PF07686) Pfam (PF07654) | Mus musculus (Mouse) | |
| 3 | C, E (A, E) | Antigen-presenting glycoprotein CD1d1 | polymer | 285 | 32632.7 | 2 | UniProt (A0A0R4J090) Pfam (PF16497) Pfam (PF07654) UniProt (by SIFTS) (P11609) | Mus musculus (Mouse) | MCG3074,isoform CRA_a |
| 4 | D, H (B, F) | Beta-2-microglobulin | polymer | 99 | 11660.4 | 2 | UniProt (P01887) Pfam (PF07654) | Mus musculus (Mouse) | |
| 5 | I, J, L, N (I, J, L, N) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 4 | In PDB GlyTouCan (G42666HT) | |||
| 6 | K, M (K, M) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 570.5 | 2 | In PDB GlyTouCan (G21290RB) | |||
| 7 | O, P, X, Y (C, D, G, H) | SODIUM ION | non-polymer | 23.0 | 4 | Chemie (NA) | |||
| 8 | Q (D) | CHLORIDE ION | non-polymer | 35.5 | 1 | Chemie (CL) | |||
| 9 | R, U (A, E) | N-{(2S,3S,4R)-1-[(4-O-benzyl-alpha-D-galactopyranosyl)oxy]-3,4-dihydroxyoctadecan-2-yl}hexacosanamide | non-polymer | 948.4 | 2 | Chemie (JTV) | |||
| 10 | S, T, V, W (A, E, G) | GLYCEROL | non-polymer | 92.1 | 4 | Chemie (GOL) | |||
| 11 | AA, BA, CA, DA, EA... (D, A, B, E, G...) | water | water | 18.0 | 253 | Chemie (HOH) |
Sequence modifications
C, G: 1 - 92 (UniProt: A0A0B4J1J9)
C, G: 93 - 112 (PDB: 6MIY)
C, G: 114 - 208 (UniProt: K7N5M3)
D, H: 0 - 94 (UniProt: A2NTY6)
D, H: 99 - 130 (UniProt: A0N8J3)
D, H: 131 - 240 (UniProt: A0A5B9)
A, E: 1 - 279 (UniProt: A0A0R4J090)
| PDB | External Database | Details |
|---|---|---|
| Met 0 | - | initiating methionine |
| Ile 113 | - | linker |
C, G: 114 - 208 (UniProt: K7N5M3)
D, H: 0 - 94 (UniProt: A2NTY6)
| PDB | External Database | Details |
|---|---|---|
| Asp 95 | - | linker |
| Glu 96 | - | linker |
| Gly 97 | - | linker |
| Tyr 98 | - | linker |
| PDB | External Database | Details |
|---|---|---|
| Ala 130 | Ala 127 | linker |
| PDB | External Database | Details |
|---|---|---|
| Cys 168 | Ser 56 | variant |
| Ser 186 | Cys 74 | variant |
| PDB | External Database | Details |
|---|---|---|
| His 280 | - | expression tag |
| His 281 | - | expression tag |
| His 282 | - | expression tag |
| His 283 | - | expression tag |
| His 284 | - | expression tag |
| His 285 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 8 |
| Total formula weight | 188751.3 | |
| Branched | Number of molecules | 6 |
| Total formula weight | 2838.7 | |
| Non-Polymers* | Number of molecules | 11 |
| Total formula weight | 2392.7 | |
| All* | Total formula weight | 193982.6 |
