4ZAK
Crystal structure of the mCD1d/DB06-1/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 | Antigen-presenting glycoprotein CD1d1 | polymer | 285 | 32632.7 | 1 | UniProt (P11609) Pfam (PF16497) Pfam (PF07654) In PDB | Mus musculus (Mouse) | |
2 | B | Beta-2-microglobulin | polymer | 99 | 11660.4 | 1 | UniProt (P01887) Pfam (PF07654) In PDB | Mus musculus (Mouse) | |
3 | C | Protein Trav11,Va14Ja18/Vb8.2,Human nkt tcr alpha chain | polymer | 209 | 23055.6 | 1 | UniProt (A0A0B4J1J9) UniProt (A0N4Z0) UniProt (K7N5M3) Pfam (PF07686) Pfam (PF09291) UniProt (by SIFTS) (A0A0G2JG46) In PDB | Mus musculus (Mouse) | Protein Trav11d,Human nkt tcr beta chain |
4 | D | T cell antigen receptor beta chain 8.2,T-cell receptor beta-2 chain C region,Protein Trbc2,T-cell receptor beta-2 chain C region | polymer | 241 | 27027.0 | 1 | UniProt (A0A075B5J4) UniProt (A0A5B9) Pfam (PF07686) Pfam (PF07654) UniProt (by SIFTS) (A2NTY6) UniProt (by SIFTS) (A0N8J3) In PDB | Mus musculus | |
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 | A | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 2 | Chemie (NAG) | |||
7 | A | N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanethioamide | non-polymer | 874.4 | 1 | Chemie (4LX) |
Sequence modifications
A: 1 - 279 (UniProt: P11609)
C: 1 - 93 (UniProt: A0A0B4J1J9)
C: 94 - 112 (UniProt: A0N4Z0)
C: 114 - 208 (UniProt: K7N5M3)
D: 0 - 112 (PDB: 4ZAK)
D: 113 - 129 (UniProt: A0A075B5J4)
D: 130 - 240 (UniProt: A0A5B9)
PDB | External Database | Details |
---|---|---|
His 201 | Asp 219 | conflict |
His 280 | - | expression tag |
His 281 | - | expression tag |
His 282 | - | expression tag |
His 283 | - | expression tag |
His 284 | - | expression tag |
His 285 | - | expression tag |
PDB | External Database | Details |
---|---|---|
Met 0 | - | initiating methionine |
PDB | External Database | Details |
---|---|---|
Ala 98 | Thr 6 | conflict |
His 103 | Tyr 11 | conflict |
Ala 106 | Arg 14 | conflict |
Ile 111 | Thr 19 | conflict |
Ile 113 | - | linker |
D: 0 - 112 (PDB: 4ZAK)
D: 113 - 129 (UniProt: A0A075B5J4)
D: 130 - 240 (UniProt: A0A5B9)
PDB | External Database | Details |
---|---|---|
Cys 168 | Ser 56 | engineered mutation |
Ser 186 | Cys 74 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 4 |
Total formula weight | 94375.6 | |
Branched | Number of molecules | 1 |
Total formula weight | 424.4 | |
Non-Polymers* | Number of molecules | 3 |
Total formula weight | 1316.8 | |
All* | Total formula weight | 96116.8 |