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Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with 6-[(3-aminopropyl)amino]-N-hydroxyhexanamide
Analyse Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UHV
- Type
- protein
- Length
- 617 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.53
- Source
- Danio rerio
- Molecule
- Polyamine deacetylase HDAC10
- EC
- 3.5.1.48, 3.5.1.62
- UniProt
- F1QCV2
- Ligands
- XS6, K, ZN, PO4
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · resolution 2.53 · 1 distinct chain · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyamine deacetylase HDAC10 (EC 3.5.1.48, 3.5.1.62) | protein | 617 | 42% helix, 14% strand | F1QCV2 |
Ligands and binding sites
- XS6 · 6-[(3-aminopropyl)amino]-N-hydroxyhexanamide · ligand · chains A
- K · Potassium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.62 | 0.83 | 41 | empty |
| 2 | 198 | 0.59 | 0.81 | 26 | empty |
| 3 | 71 | 0.53 | 0.86 | 16 | empty |
| 4 | 92 | 0.45 | 0.80 | 23 | empty |
| 5 | 58 | 0.31 | 0.76 | 14 | empty |
Compared structures
- 6UHV · Crystal structure of danio rerio histone deacetylase 10 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- F1QCV2 · AlphaFold monomer V2.0 prediction for polyamine deacetylase HDAC10 (F1QCV2) · a predicted model of the same protein · 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 F1QCV2
- Elsewhere: RCSB PDB 6UHV · PDBe 6UHV · UniProt F1QCV2
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