MolNFT v1 · #117669 · protein
Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in complex with hpob
5EF7 · HDAC6 protein: “Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in complex with hpob”. X-ray diffraction, 3 ligands (5OJ, K, ZN), 4 pockets (best druggability 0.62). MolNFT v1 #117669 on GenesisL1: 3D…
- PDB
- 5EF7
- Type
- protein
- Length
- 714 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HDAC6 protein
- EC
- 3.5.1.98
- UniProt
- A7YT55
- Ligands
- 5OJ, K, ZN
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HDAC6 protein (EC 3.5.1.98) | protein | 358 | 43% helix, 14% strand | A7YT55 |
| B | HDAC6 protein (EC 3.5.1.98) | protein | 356 | 43% helix, 14% strand | A7YT55 |
Ligands and binding sites
- 5OJ · 4-[2-[2-hydroxyethyl(phenyl)amino]-2-oxidanylidene-ethyl]-~{N}-oxidanyl-benzamide · 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.62 | 0.79 | 39 | 5OJ |
| 2 | 122 | 0.53 | 0.82 | 22 | empty |
| 3 | 80 | 0.48 | 0.83 | 20 | empty |
| 4 | 101 | 0.39 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 496 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5EF7 · Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex 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 5EF7 · PDBe 5EF7 · UniProt A7YT55
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