MolNFT v1 · #117648 · protein
Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2
5EEM · HDAC6 protein: “Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2”. X-ray diffraction, 3 ligands (K, ZN, NA), 4 pockets (best druggability 0.60). MolNFT v1 #117648 on GenesisL1: 3D structure, binding sites…
- PDB
- 5EEM
- Type
- protein
- Length
- 707 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, NA
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | HDAC6 protein (EC 3.5.1.98) | protein | 353 | 43% helix, 14% strand | A7YT55 |
| A | HDAC6 protein (EC 3.5.1.98) | protein | 354 | 44% helix, 13% strand | A7YT55 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains B, A
- ZN · Zinc ion · metal · 2 copies · chains B, A
- NA · Sodium ion · metal · chains B
- FMT · Formic acid · additive · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.60 | 0.78 | 48 | empty |
| 2 | 96 | 0.50 | 0.82 | 21 | empty |
| 3 | 121 | 0.49 | 0.80 | 20 | empty |
| 4 | 103 | 0.37 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- B–A · 519 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5EEM · Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 · 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 5EEM · PDBe 5EEM · UniProt A7YT55
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