MolNFT v1 · #77937 · protein
Structure of the mouse CD1D-HS44-inkt TCR complex
3RTQ · Antigen-presenting glycoprotein CD1D1: “Structure of the mouse CD1D-HS44-inkt TCR complex”. X-ray diffraction, 4 ligands (H4S, NAG, BMA), 7 pockets (best druggability 0.87). MolNFT v1 #77937 on GenesisL1: 3D structure, binding sites…
- PDB
- 3RTQ
- Type
- protein
- Length
- 806 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
- H4S, NAG, BMA, FUL
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 268 | 26% helix, 40% strand | P11609 |
| B | Beta-2-microglobulin | protein | 96 | 0% helix, 51% strand | P01887 |
| C | VALPHA14 (mouse variable domain, human constant domain) | protein | 203 | 3% helix, 47% strand | — |
| D | V BETA8.2 (mouse variable domain, human constant domain) | protein | 239 | 6% helix, 49% strand | — |
Ligands and binding sites
- H4S · N-[(2S,3S,4R)-3,4-dihydroxy-1-{[(1S,2S,3R,4R,5S)-2,3,4,5-tetrahydroxycyclohexyl]amino}octadecan-2-yl]hexacosanamide · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- FUL · beta-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.87 | 0.88 | 75 | H4S |
| 2 | 921 | 0.69 | 0.75 | 69 | empty |
| 3 | 329 | 0.63 | 0.79 | 44 | empty |
| 4 | 186 | 0.50 | 0.77 | 28 | empty |
| 5 | 108 | 0.40 | 0.76 | 22 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2203 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1165 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 479 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 390 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3RTQ · Structure of the mouse CD1d-HS44-iNKT TCR complex · the same entry in another collection · chain D against D, TM-score 1.00
- 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 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
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 3RTQ · PDBe 3RTQ · UniProt P11609 · UniProt P01887
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