MolNFT v1 · #91243 · protein
Crystal structure of bovine CD1D with bound C16:0-alpha-galactosyl ceramide
4F7E · CD1D antigen, D polypeptide: “Crystal structure of bovine CD1D with bound C16:0-alpha-galactosyl ceramide”. X-ray diffraction, 3 ligands (0SH, NAG, SO4), 3 pockets (best druggability 0.85). MolNFT v1 #91243 on GenesisL1: 3D…
- PDB
- 4F7E
- Type
- protein
- Length
- 369 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD1D antigen, D polypeptide; Beta-2-microglobulin
- UniProt
- A1L565, P01888
- Ligands
- 0SH, NAG, SO4
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CD1D antigen, D polypeptide | protein | 271 | 25% helix, 41% strand | A1L565 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P01888 |
Ligands and binding sites
- 0SH · N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]hexadecanamide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.85 | 0.90 | 53 | 0SH |
| 2 | 270 | 0.58 | 0.78 | 35 | empty |
| 3 | 88 | 0.38 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1489 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4F7E · Crystal structure of bovine CD1d with bound C16:0-alpha-galactosyl ceramide · the same entry in another collection · chain A against A, TM-score 1.00
- P01888 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01888) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 A1L565
- Every structure of UniProt P01888
- Elsewhere: RCSB PDB 4F7E · PDBe 4F7E · UniProt A1L565 · UniProt P01888
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