Research workbench
Structure of mouse VA14VB8.2NKT TCR-mouse CD1D-a-C-galactosylceramide complex
Analyse Structure of mouse VA14VB8.2NKT TCR-mouse CD1D-a-C-galactosylceramide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TN0
- Type
- protein
- Length
- 829 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2 microglobulin; Mouse nkt VALPHA14 (mouse…
- UniProt
- P11609, Q91XJ8
- Ligands
- QUX, NAG
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 293 | 27% helix, 39% strand | P11609 |
| B | Beta-2 microglobulin | protein | 98 | 0% helix, 48% strand | Q91XJ8 |
| C | Mouse nkt VALPHA14 (mouse variable domain, human constant domain) | protein | 203 | 3% helix, 46% strand | — |
| D | Mouse nkt VBETA8.2 (mouse variable domain, human constant domain) | protein | 235 | 7% helix, 49% strand | — |
Ligands and binding sites
- QUX · N-[(3S,4S,5R)-4,5-dihydroxy-1-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]nonadecan-3-yl]hexacosanamide · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.86 | 0.87 | 80 | QUX |
| 2 | 871 | 0.69 | 0.75 | 67 | empty |
| 3 | 319 | 0.62 | 0.79 | 39 | empty |
| 4 | 89 | 0.54 | 0.85 | 22 | empty |
| 5 | 176 | 0.52 | 0.78 | 27 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1942 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1774 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 377 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 227 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3TN0 · Structure of mouse Va14Vb8.2NKT TCR-mouse CD1d-a-C-Galactosylceramide complex · the same entry in another collection · chain A against A, 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 0.94
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 Q91XJ8
- Elsewhere: RCSB PDB 3TN0 · PDBe 3TN0 · UniProt P11609 · UniProt Q91XJ8
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