MolNFT v1 · #117683 · protein
Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 (H574A) in complex with histone H4 LYS6 tripeptide substrate
5EFN · HDAC6 protein: “Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 (H574A) in complex with histone H4…”. X-ray diffraction, 3 ligands (MCM, K, ZN), 2 pockets (best druggability 0.52). MolNFT v1 #117683 on…
- PDB
- 5EFN
- Type
- protein
- Length
- 720 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HDAC6 protein; Histone H4 tripeptide
- EC
- 3.5.1.98
- UniProt
- A7YT55
- Ligands
- MCM, K, ZN
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | HDAC6 protein (EC 3.5.1.98) | protein | 357 | 43% helix, 14% strand | A7YT55 |
| F, E | Histone H4 tripeptide | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- MCM · 7-amino-4-methyl-chromen-2-one · ligand · 2 copies · chains B, F, A, E
- K · Potassium ion · metal · 4 copies · chains B, A
- ZN · Zinc ion · metal · 2 copies · chains B, F, A, E
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.52 | 0.75 | 40 | empty |
| 2 | 207 | 0.42 | 0.72 | 31 | empty |
Interfaces
3 interfaces between chains.
- B–A · 339 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 289 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 289 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 5EFN · Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (H574A) in… · the same entry in another collection · chain B against B, 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 5EFN · PDBe 5EFN · UniProt A7YT55
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.