6MJI
Crystal structure of the mCD1d/xxs (JJ304) /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 | C | T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN | polymer | 209 | 23055.6 | 1 | UniProt (A0A0B4J1J9) UniProt (K7N5M3) Pfam (PF07686) Pfam (PF09291) In PDB | Mus musculus (Mouse) | T cell receptor alpha variable 11D, Human nkt tcr beta chain |
| 2 | D | Beta-chain,Tcell receptor chain,T cell receptor beta constant 2 | polymer | 241 | 27027.0 | 1 | UniProt (A2NTY6) UniProt (A0N8J3) UniProt (A0A5B9) Pfam (PF07686) Pfam (PF07654) In PDB | Mus musculus (Mouse) | |
| 3 | A | Antigen-presenting glycoprotein CD1d1 | polymer | 285 | 32632.7 | 1 | UniProt (A0A0R4J090) Pfam (PF16497) Pfam (PF07654) UniProt (by SIFTS) (P11609) In PDB | Mus musculus (Mouse) | MCG3074,isoform CRA_a |
| 4 | B | Beta-2-microglobulin | polymer | 99 | 11660.4 | 1 | UniProt (P01887) Pfam (PF07654) In PDB | Mus musculus (Mouse) | |
| 5 | E | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 1 | In PDB GlyTouCan (G42666HT) | |||
| 6 | F | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 894.8 | 1 | In PDB GlyTouCan (G42466VF) | |||
| 7 | C, D | SODIUM ION | non-polymer | 23.0 | 2 | Chemie (NA) | |||
| 8 | D, A, B | GLYCEROL | non-polymer | 92.1 | 6 | Chemie (GOL) | |||
| 9 | A | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 1 | Chemie (NAG) | |||
| 10 | A | N-[(2S,3S,4R)-1-{[4-O-(cyclopropylmethyl)-alpha-D-galactopyranosyl]oxy}-3,4-dihydroxyoctadecan-2-yl]hexacosanamide | non-polymer | 912.4 | 1 | Chemie (JTD) | |||
| 11 | water | water | 18.0 | 396 | Chemie (HOH) |
Sequence modifications
C: 1 - 92 (UniProt: A0A0B4J1J9)
C: 93 - 112 (PDB: 6MJI)
C: 114 - 208 (UniProt: K7N5M3)
D: 0 - 94 (UniProt: A2NTY6)
D: 99 - 130 (UniProt: A0N8J3)
D: 131 - 240 (UniProt: A0A5B9)
A: 1 - 279 (UniProt: A0A0R4J090)
| PDB | External Database | Details |
|---|---|---|
| Met 0 | - | initiating methionine |
| Ile 113 | - | linker |
C: 114 - 208 (UniProt: K7N5M3)
D: 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 | 4 |
| Total formula weight | 94375.6 | |
| Branched | Number of molecules | 2 |
| Total formula weight | 1319.2 | |
| Non-Polymers* | Number of molecules | 10 |
| Total formula weight | 1732.2 | |
| All* | Total formula weight | 97427.0 |
