Research workbench
Structure of the mus musclus langerin carbohydrate recognition domain
Analyse Structure of the mus musclus langerin carbohydrate recognition domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K8Y
- Type
- protein
- Length
- 272 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-type lectin domain family 4 member K
- UniProt
- Q8VBX4
- Ligands
- CA
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | C-type lectin domain family 4 member K | protein | 136 | 25% helix, 29% strand | Q8VBX4 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- P6G · Hexaethylene glycol · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.48 | 0.78 | 23 | P6G |
Interfaces
1 interface between chains.
- A–B · 761 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5K8Y · Structure of the Mus musclus Langerin carbohydrate recognition domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q8VBX4 · AlphaFold monomer V2.0 prediction for C-type lectin domain family 4 member K (Q8VBX4) · a predicted model of the same protein · chain A 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 Q8VBX4
- Elsewhere: RCSB PDB 5K8Y · PDBe 5K8Y · UniProt Q8VBX4
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