MolNFT v1 · #58044 · protein
Ternary crystal structure of the mouse nkt TCR-CD1D-3'DEOXY-alpha- galactosylceramide
3ARD · Antigen-presenting glycoprotein CD1D1: “Ternary crystal structure of the mouse nkt TCR-CD1D-3'DEOXY-alpha- galactosylceramide”. X-ray diffraction, 2 ligands (3GH, NAG), 10 pockets (best druggability 0.86). MolNFT v1 #58044 on…
- PDB
- 3ARD
- Type
- protein
- Length
- 833 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; Nkt VALPHA14-JALPHA18,NKT…
- UniProt
- P11609, P01887
- Ligands
- 3GH, NAG
- Pockets
- 10 · best druggability 0.86
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 | 294 | 27% helix, 38% strand | P11609 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C | Nkt VALPHA14-JALPHA18,NKT VALPHA14-JALPHA18 | protein | 202 | 1% helix, 47% strand | — |
| D | VBETA8.2,VBETA8.2 | protein | 238 | 6% helix, 49% strand | — |
Ligands and binding sites
- 3GH · N-{(2S,3R)-1-[(3-deoxy-alpha-D-xylo-hexopyranosyl)oxy]-3-hydroxyoctadecan-2-yl}hexacosanamide · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.86 | 0.88 | 75 | 3GH |
| 2 | 727 | 0.66 | 0.75 | 69 | empty |
| 3 | 385 | 0.62 | 0.77 | 42 | empty |
| 4 | 187 | 0.52 | 0.78 | 35 | empty |
| 5 | 192 | 0.49 | 0.76 | 30 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2027 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1766 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 482 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 192 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3ARD · Ternary crystal structure of the mouse NKT TCR-CD1d-3'deoxy-alpha-galactosylceramide · 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 0.98
- 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 3ARD · PDBe 3ARD · UniProt P11609 · UniProt P01887
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