MolNFT v1 · #58047 · protein
Ternary crystal structure of the mouse nkt TCR-CD1D-alpha- GLUCOSYLCERAMIDE(C20:2)
3ARG · Antigen-presenting glycoprotein CD1D1: “Ternary crystal structure of the mouse nkt TCR-CD1D-alpha- GLUCOSYLCERAMIDE(C20:2)”. X-ray diffraction, 2 ligands (DB6, NAG), 11 pockets (best druggability 0.85). MolNFT v1 #58047 on…
- PDB
- 3ARG
- Type
- protein
- Length
- 826 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
- DB6, NAG
- Pockets
- 11 · best druggability 0.85
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 | 26% helix, 37% strand | P11609 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P01887 |
| C | Nkt VALPHA14-JALPHA18,NKT VALPHA14-JALPHA18 | protein | 202 | 1% helix, 48% strand | — |
| D | VBETA8.2,VBETA8.2 | 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 · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.85 | 0.86 | 95 | DB6 |
| 2 | 367 | 0.60 | 0.77 | 38 | empty |
| 3 | 356 | 0.55 | 0.74 | 43 | empty |
| 4 | 186 | 0.52 | 0.78 | 30 | empty |
| 5 | 279 | 0.51 | 0.74 | 30 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1851 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1664 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 334 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 190 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3ARG · Ternary crystal structure of the mouse NKT TCR-CD1d-alpha-glucosylceramide(C20:2) · 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 3ARG · PDBe 3ARG · UniProt P11609 · UniProt P01887
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