MolNFT v1 · #78580 · protein
Crystal structure of autoreactive-VALPHA14-VBETA6 nkt TCR in complex with CD1D-beta-galactosylceramide
3SDA · Antigen-presenting glycoprotein CD1D1: “Crystal structure of autoreactive-VALPHA14-VBETA6 nkt TCR in complex with CD1D-beta-galactosylceramide”. X-ray diffraction, 2 ligands (GCY, NAG), 13 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 3SDA
- 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; Nkt TCR VALPHA14 chain; Nkt…
- UniProt
- P11609, P01887
- Ligands
- GCY, NAG
- Pockets
- 13 · 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 | 290 | 28% helix, 39% strand | P11609 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C | Nkt TCR VALPHA14 chain | protein | 196 | 2% helix, 46% strand | — |
| D | Nkt TCR autoreactive-VBETA6 chain | protein | 239 | 5% helix, 49% strand | — |
Ligands and binding sites
- GCY · N-[(2S,3R)-1-(beta-D-galactopyranosyloxy)-3-hydroxyoctadec-4-en-2-yl]tetracosanamide · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.86 | 0.87 | 77 | GCY |
| 2 | 880 | 0.69 | 0.75 | 70 | empty |
| 3 | 461 | 0.67 | 0.79 | 55 | GOL |
| 4 | 55 | 0.55 | 0.89 | 22 | empty |
| 5 | 164 | 0.54 | 0.80 | 34 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2173 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1626 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 455 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 304 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan, 1 covalent (disulfide, N-glycosylation, additive adduct).
Compared structures
- 3SDA · Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with… · 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 0.96
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 3SDA · PDBe 3SDA · UniProt P11609 · UniProt P01887
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