Research workbench
Recognition of glycolipid antigen by inkt cell TCR
Analyse Recognition of glycolipid antigen by inkt cell TCR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O8X
- Type
- protein
- Length
- 806 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; VALPHA14 chimera (mouse…
- UniProt
- P11609, P01887, P01848, A0A5B9
- Ligands
- GSL, NAG, FUC
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 268 | 27% helix, 39% strand | P11609 |
| B | Beta-2-microglobulin | protein | 96 | 0% helix, 51% strand | P01887 |
| C | VALPHA14 chimera (mouse variable domain, human T-cell receptor alpha chain C region constant domain) | protein | 203 | 3% helix, 48% strand | P01848 |
| D | VBETA8.2 chimera (mouse variable domain, human T-cell receptor beta-2 chain C region constant domain) | protein | 239 | 6% helix, 49% strand | A0A5B9 |
Ligands and binding sites
- GSL · (2S,3R)-3-hydroxy-2-(tetradecanoylamino)octadecyl alpha-D-galactopyranosiduronic acid · ligand · chains A, C
- 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 | 876 | 0.87 | 0.88 | 73 | GSL |
| 2 | 920 | 0.70 | 0.75 | 70 | empty |
| 3 | 353 | 0.63 | 0.79 | 44 | empty |
| 4 | 152 | 0.46 | 0.76 | 22 | empty |
| 5 | 128 | 0.45 | 0.77 | 28 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2082 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1091 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 490 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 355 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3O8X · Recognition of Glycolipid Antigen by iNKT Cell TCR · the same entry in another collection · chain D against D, TM-score 1.00
- P11609 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D1 (P11609) · a predicted model of the same protein · chain A against A, 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
- A0A5B9 · AlphaFold monomer V2.0 prediction for T cell receptor beta constant 2 (A0A5B9) · a predicted model of the same protein · chain D against A, TM-score 0.53
- P01848 · AlphaFold monomer V2.0 prediction for T cell receptor alpha chain constant (P01848) · a predicted model of the same protein · chain C against A, TM-score 0.43
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 P11609
- Every structure of UniProt P01887
- Every structure of UniProt P01848
- Every structure of UniProt A0A5B9
- Elsewhere: RCSB PDB 3O8X · PDBe 3O8X · UniProt P11609 · UniProt P01887 · UniProt P01848 · UniProt A0A5B9
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