MolNFT v1 · #168826 · protein
Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 complexed with cyclopeptide DES4.3.1
6WSJ · HDAC6 protein: “Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 complexed with cyclopeptide DES4.3.1”. X-ray diffraction, 2 ligands (K, ZN), 1 pocket (best druggability 0.31). MolNFT v1 #168826 on…
- PDB
- 6WSJ
- Type
- protein
- Length
- 360 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HDAC6 protein; Cyclopeptide DES4.3.1
- UniProt
- A7YT55
- Ligands
- K, ZN
- Pockets
- 1 · best druggability 0.31
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HDAC6 protein | protein | 352 | 44% helix, 14% strand | A7YT55 |
| I | Cyclopeptide DES4.3.1 | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A, I
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, I
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 | 58 | 0.31 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–I · 386 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 d-amino, 2 modified (D-amino acid, nonstandard).
Compared structures
- 6WSJ · Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with… · 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 A7YT55
- Elsewhere: RCSB PDB 6WSJ · PDBe 6WSJ · UniProt A7YT55
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