Research workbench
Recognition of a glycolipid antigen by the inkt cell TCR
Analyse Recognition of a glycolipid antigen by the 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
- 3O9W
- Type
- protein
- Length
- 813 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
- 1O2, NAG, FUC
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 274 | 25% helix, 41% strand | P11609 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 53% strand | P01887 |
| C | VALPHA14 chimera (mouse variable domain, human T-cell receptor alpha chain C region constant domain) | protein | 203 | 3% helix, 47% 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
- 1O2 · (2S)-3-(alpha-D-galactopyranosyloxy)-2-(hexadecanoyloxy)propyl (9Z)-octadec-9-enoate · 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 | 973 | 0.85 | 0.86 | 81 | 1O2 |
| 2 | 978 | 0.70 | 0.75 | 70 | empty |
| 3 | 454 | 0.67 | 0.79 | 54 | empty |
| 4 | 175 | 0.48 | 0.76 | 23 | empty |
| 5 | 153 | 0.45 | 0.76 | 28 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2155 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1238 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 473 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 368 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3O9W · Recognition of a Glycolipid Antigen by the 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 3O9W · PDBe 3O9W · UniProt P11609 · UniProt P01887 · UniProt P01848 · UniProt A0A5B9
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