MolNFT v1 · #145714 · protein
Structure of alpha-GC[8,16P] bound by CD1D and in complex with the VA14VB8.2 TCR
6CW9 · Chimeric T cell antigen receptor alpha chain. VA14,VA24…: “Structure of alpha-GC[8,16P] bound by CD1D and in complex with the VA14VB8.2 TCR”. X-ray diffraction, 4 ligands (PLM, 7LM, NAG), 8 pockets (best druggability 0.86). MolNFT…
- PDB
- 6CW9
- Type
- protein
- Length
- 813 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimeric T cell antigen receptor alpha chain. VA14,VA24, JA18; Chimeric T cell antigen…
- UniProt
- A0A0R4J090, P01887
- Ligands
- PLM, 7LM, NAG, FUC
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Chimeric T cell antigen receptor alpha chain. VA14,VA24, JA18 | protein | 203 | 5% helix, 48% strand | — |
| D | Chimeric T cell antigen receptor beta chain VB8.2, VB11 | protein | 239 | 6% helix, 49% strand | — |
| A | Antigen-presenting glycoprotein CD1D1 | protein | 274 | 27% helix, 41% strand | A0A0R4J090 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 51% strand | P01887 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A
- 7LM · N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxy-16-phenylhexadecan-2-yl]octanamide · ligand · chains C, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.86 | 0.87 | 71 | PLM, 7LM |
| 2 | 852 | 0.67 | 0.74 | 68 | empty |
| 3 | 436 | 0.66 | 0.78 | 47 | empty |
| 4 | 173 | 0.49 | 0.77 | 23 | empty |
| 5 | 151 | 0.46 | 0.76 | 27 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2140 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1202 Ų buried · 10 hydrogen bonds · protein-protein
- C–A · 469 Ų buried · 9 hydrogen bonds · protein-protein
- D–A · 344 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6CW9 · Structure of alpha-GC[8,16P] bound by CD1d and in complex with the Va14Vb8.2 TCR · the same entry in another collection · chain C against C, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A0R4J090
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 6CW9 · PDBe 6CW9 · UniProt A0A0R4J090 · UniProt P01887
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