Research workbench
Crystal Structure of the Human CLEC9A C-type Lectin-Like Domain
Analyse Crystal Structure of the Human CLEC9A C-type Lectin-Like Domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VPP
- Type
- protein
- Length
- 243 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.642
- Source
- Homo sapiens
- Molecule
- C-type lectin domain family 9 member A
- UniProt
- Q6UXN8
- Ligands
- CA
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · resolution 1.642 · 2 distinct chains · 17% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-type lectin domain family 9 member A | protein | 121 | 17% helix, 35% strand | Q6UXN8 |
| B | C-type lectin domain family 9 member A | protein | 122 | 17% helix, 34% strand | Q6UXN8 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.69 | 0.78 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 316 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3VPP · Crystal structure of the human CLEC9A C-type lectin-like domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q6UXN8 · AlphaFold monomer V2.0 prediction for C-type lectin domain family 9 member a (Q6UXN8) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q6UXN8
- Elsewhere: RCSB PDB 3VPP · PDBe 3VPP · UniProt Q6UXN8
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