MolNFT v1 · #160974 · protein
Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 complexed with ap-1-62-a
6PZU · HDAC6 protein: “Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 complexed with ap-1-62-a”. X-ray diffraction, 3 ligands (A6I, K, ZN), 2 pockets (best druggability 0.51). MolNFT v1 #160974 on GenesisL1: 3D…
- PDB
- 6PZU
- Type
- protein
- Length
- 714 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HDAC6 protein
- UniProt
- A7YT55
- Ligands
- A6I, K, ZN
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | HDAC6 protein | protein | 357 | 44% helix, 14% strand | A7YT55 |
Ligands and binding sites
- A6I · N-[(benzyloxy)carbonyl]-L-leucyl-N-{[4-(hydroxycarbamoyl)phenyl]methyl}-L-alaninamide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.51 | 0.75 | 45 | empty |
| 2 | 88 | 0.31 | 0.72 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 339 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6PZU · 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 6PZU · PDBe 6PZU · UniProt A7YT55
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