Research workbench
Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in complex with acetate
Analyse Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EFG
- Type
- protein
- Length
- 715 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
- K, ZN
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | HDAC6 protein (EC 3.5.1.98) | protein | 357 | 43% helix, 13% strand | A7YT55 |
| A | HDAC6 protein (EC 3.5.1.98) | protein | 358 | 43% helix, 14% strand | A7YT55 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains D, A
- ZN · Zinc ion · metal · 2 copies · chains D, A
- ACT · Acetate ion · additive · 2 copies · chains D, 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.46 | 0.77 | 19 | empty |
| 2 | 131 | 0.41 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- D–A · 339 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5EFG · Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with… · the same entry in another collection · chain D against D, 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 5EFG · PDBe 5EFG · UniProt A7YT55
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