Research workbench
Crystal structure of danio rerio histone deacetylase 10 H137A mutant in complex with N-acetylputrescine (tetrahedral intermediate)
Analyse Crystal structure of danio rerio histone deacetylase 10 H137A mutant in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KUT
- Type
- protein
- Length
- 643 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyamine deacetylase HDAC10
- EC
- 3.5.1.48, 3.5.1.62
- UniProt
- F1QCV2
- Ligands
- X51, K, ZN, NA, PO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyamine deacetylase HDAC10 (EC 3.5.1.48, 3.5.1.62) | protein | 643 | 42% helix, 15% strand | F1QCV2 |
Ligands and binding sites
- X51 · 1-[(4-aminobutyl)amino]ethane-1,1-diol · ligand · chains A
- K · Potassium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 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 | 129 | 0.70 | 0.91 | 34 | empty |
| 2 | 216 | 0.65 | 0.84 | 36 | PEG, EDO |
| 3 | 131 | 0.57 | 0.83 | 20 | empty |
| 4 | 52 | 0.34 | 0.78 | 22 | PO4 |
| 5 | 56 | 0.31 | 0.76 | 18 | EDO |
Compared structures
- 7KUT · Crystal Structure of Danio rerio Histone Deacetylase 10 H137A Mutant 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 7KUT · PDBe 7KUT · UniProt F1QCV2
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