Research workbench
Structure of the carbohydrate-recognition domain of the C-type lectin mincle bound to trehalose
Analyse Structure of the carbohydrate-recognition domain of the C-type lectin mincle… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KZV
- Type
- protein
- Length
- 258 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-type lectin mincle
- UniProt
- E1BHM0
- Ligands
- GLC, CA, NA
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-type lectin mincle | protein | 131 | 18% helix, 27% strand | E1BHM0 |
| B | C-type lectin mincle | protein | 127 | 18% helix, 33% strand | E1BHM0 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.49 | 0.84 | 19 | empty |
| 2 | 58 | 0.26 | 0.72 | 18 | NA |
Interfaces
1 interface between chains.
- A–B · 409 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4KZV · Structure of the carbohydrate-recognition domain of the C-type lectin mincle bound to… · the same entry in another collection · chain A against A, TM-score 1.00
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 E1BHM0
- Elsewhere: RCSB PDB 4KZV · PDBe 4KZV · UniProt E1BHM0
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