Research workbench
Crystal structure of mouse CD1D-alpha-galactosylceramide with mouse VALPHA14-VBETA8.2 nkt TCR
Analyse Crystal structure of mouse CD1D-alpha-galactosylceramide with mouse… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HE6
- Type
- protein
- Length
- 824 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; VALPHA14(MOUSE variable…
- UniProt
- P11609, P01887
- Ligands
- AGH, NAG
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 286 | 26% helix, 39% strand | P11609 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 47% strand | P01887 |
| C | VALPHA14(MOUSE variable domain, human constant domain) | protein | 203 | 3% helix, 48% strand | — |
| D | VBETA8.2(MOUSE variable domain, human constant domain) | protein | 236 | 7% helix, 49% strand | — |
Ligands and binding sites
- AGH · N-{(1S,2R,3S)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.84 | 0.85 | 78 | AGH |
| 2 | 893 | 0.69 | 0.75 | 67 | empty |
| 3 | 431 | 0.66 | 0.78 | 48 | empty |
| 4 | 178 | 0.55 | 0.80 | 29 | empty |
| 5 | 180 | 0.46 | 0.75 | 26 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2015 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1908 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 479 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 210 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3HE6 · Crystal structure of mouse CD1d-alpha-galactosylceramide with mouse Valpha14-Vbeta8.2 NKT… · the same entry in another collection · 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 0.97
- 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 P01887
- Elsewhere: RCSB PDB 3HE6 · PDBe 3HE6 · UniProt P11609 · UniProt P01887
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