Research workbench
Structure of a microbial glycosphingolipid bound to mouse CD1D
Analyse Structure of a microbial glycosphingolipid bound to mouse CD1D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FIK
- Type
- protein
- Length
- 362 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD1D1; B(2)-microglobulin
- UniProt
- P11609
- Ligands
- GSL, PLM, NAG
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1D1 | protein | 265 | 26% helix, 44% strand | P11609 |
| B | B(2)-microglobulin | protein | 97 | 0% helix, 51% strand | — |
Ligands and binding sites
- GSL · (2S,3R)-3-hydroxy-2-(tetradecanoylamino)octadecyl alpha-D-galactopyranosiduronic acid · ligand · chains A
- PLM · Palmitic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.84 | 0.88 | 53 | GSL, PLM |
| 2 | 400 | 0.64 | 0.78 | 47 | empty |
| 3 | 153 | 0.46 | 0.76 | 26 | empty |
| 4 | 131 | 0.45 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1258 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 2FIK · Structure of a microbial glycosphingolipid bound to mouse CD1d · 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 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 P11609
- Elsewhere: RCSB PDB 2FIK · PDBe 2FIK · UniProt P11609
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