Research workbench
Structure of mouse CD1D with bound glycosphingolipid JJ112
Analyse Structure of mouse CD1D with bound glycosphingolipid JJ112 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TW5
- Type
- protein
- Length
- 369 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin
- UniProt
- P11609, P01887
- Ligands
- PLM, 7LM, NAG
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 273 | 26% helix, 41% strand | P11609 |
| B | Beta-2-microglobulin | protein | 96 | 0% helix, 51% strand | P01887 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A
- 7LM · N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxy-16-phenylhexadecan-2-yl]octanamide · 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.87 | 0.91 | 59 | PLM, 7LM |
| 2 | 346 | 0.63 | 0.78 | 46 | empty |
| 3 | 196 | 0.50 | 0.76 | 28 | empty |
| 4 | 117 | 0.46 | 0.79 | 26 | empty |
| 5 | 54 | 0.31 | 0.75 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 1231 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5TW5 · Structure of mouse CD1d with bound glycosphingolipid JJ112 · 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
- 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 5TW5 · PDBe 5TW5 · UniProt P11609 · UniProt P01887
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