MolNFT v1 · #90564 · protein
Crystal structure of a human VALPHA24(-) nkt TCR in complex with CD1D/ALPHA-galactosylceramide
4EN3 · Antigen-presenting glycoprotein CD1D: “Crystal structure of a human VALPHA24(-) nkt TCR in complex with CD1D/ALPHA-galactosylceramide”. X-ray diffraction, 3 ligands (AGH, NAG, FUC), 9 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 4EN3
- Type
- protein
- Length
- 782 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D; Human nkt TCR alpha chain; Human nkt TCR beta…
- UniProt
- P15813, P61769
- Ligands
- AGH, NAG, FUC
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Antigen-presenting glycoprotein CD1D | protein | 257 | 26% helix, 38% strand | P15813 |
| A | Human nkt TCR alpha chain | protein | 186 | 3% helix, 42% strand | — |
| B | Human nkt TCR beta chain | protein | 240 | 6% helix, 47% strand | — |
| D | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
Ligands and binding sites
- AGH · N-{(1S,2R,3S)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}hexacosanamide · ligand · chains C, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains C, A, B
- FUC · alpha-L-fucopyranose · sugar
- GOL · Glycerol · additive · 2 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.87 | 0.90 | 74 | AGH |
| 2 | 742 | 0.70 | 0.77 | 79 | empty |
| 3 | 361 | 0.62 | 0.78 | 47 | empty |
| 4 | 150 | 0.43 | 0.75 | 20 | empty |
| 5 | 94 | 0.43 | 0.78 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2271 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1325 Ų buried · 24 hydrogen bonds · protein-protein
- C–A · 467 Ų buried · 7 hydrogen bonds · protein-protein
- C–B · 239 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4EN3 · Crystal structure of a human Valpha24(-) NKT TCR in complex with… · the same entry in another collection · chain C against C, TM-score 1.00
- P15813 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D (P15813) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P15813
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 4EN3 · PDBe 4EN3 · UniProt P15813 · UniProt P61769
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