MolNFT v1 · #77961 · protein
Crystal structure of VALPHA10-VBETA8.1 nkt TCR in complex with CD1D- alphaglucosylceramide (C20:2)
3RUG · Antigen-presenting glycoprotein CD1D1: “Crystal structure of VALPHA10-VBETA8.1 nkt TCR in complex with CD1D- alphaglucosylceramide (C20:2)”. X-ray diffraction, 2 ligands (DB6, NAG), 20 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 3RUG
- Type
- protein
- Length
- 1,635 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; VALPHA10(MOUSE variable…
- UniProt
- P11609, P01887
- Ligands
- DB6, NAG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 286 | 28% helix, 41% strand | P11609 |
| B, D | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P01887 |
| C | Antigen-presenting glycoprotein CD1D1 | protein | 285 | 28% helix, 41% strand | P11609 |
| E, G | VALPHA10(MOUSE variable domain, human constant domain) | protein | 198 | 2% helix, 43% strand | — |
| F, H | VBETA8.1(MOUSE variable domain, human constant domain) | protein | 236 | 7% helix, 50% strand | — |
Ligands and binding sites
- DB6 · (11E,14E)-N-[(2S,3S,4R)-1-(alpha-D-glucopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide · ligand · 2 copies · chains A, E, C, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.87 | 0.90 | 66 | DB6 |
| 2 | 958 | 0.86 | 0.86 | 95 | DB6 |
| 3 | 884 | 0.75 | 0.79 | 80 | empty |
| 4 | 965 | 0.71 | 0.75 | 87 | empty |
| 5 | 875 | 0.70 | 0.75 | 85 | empty |
Interfaces
12 interfaces between chains.
- E–F · 2209 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2057 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1644 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1627 Ų buried · 24 hydrogen bonds · protein-protein
- E–H · 612 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3RUG · Crystal structure of Valpha10-Vbeta8.1 NKT TCR in complex with CD1d-alphaglucosylceramide… · the same entry in another collection · chain H against H, 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 0.95
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 3RUG · PDBe 3RUG · UniProt P11609 · UniProt P01887
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.