MolNFT v1 · #95479 · protein
Structure of the mouse CD1D-4CLPHC-alpha-galcer-inkt TCR complex
4IRJ · Antigen-presenting glycoprotein CD1D1: “Structure of the mouse CD1D-4CLPHC-alpha-galcer-inkt TCR complex”. X-ray diffraction, 3 ligands (1L9, NAG, FUC), 9 pockets (best druggability 0.86). MolNFT v1 #95479 on GenesisL1: 3D…
- PDB
- 4IRJ
- Type
- protein
- Length
- 804 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
- 1L9, NAG, FUC
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 267 | 27% helix, 39% strand | P11609 |
| B | Beta-2-microglobulin | protein | 96 | 0% helix, 51% strand | P01887 |
| C | VALPHA14 (mouse variable domain, human constant domain) | protein | 202 | 4% helix, 48% strand | — |
| D | VBETA8.2 (mouse variable domain, human constant domain) | protein | 239 | 6% helix, 49% strand | — |
Ligands and binding sites
- 1L9 · N-[(2S,3S,4R)-1-({6-O-[(4-chlorophenyl)carbamoyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.86 | 0.87 | 77 | 1L9 |
| 2 | 333 | 0.62 | 0.78 | 44 | empty |
| 3 | 575 | 0.62 | 0.74 | 49 | empty |
| 4 | 219 | 0.49 | 0.75 | 29 | empty |
| 5 | 219 | 0.48 | 0.75 | 26 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2098 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1110 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 484 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 337 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4IRJ · Structure of the mouse CD1d-4ClPhC-alpha-GalCer-iNKT TCR complex · the same entry in another collection · chain A against A, 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 4IRJ · PDBe 4IRJ · UniProt P11609 · UniProt P01887
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