MolNFT v1 · #137998 · protein
Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in complex with KV70
5W5K: “Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in complex with KV70”. X-ray diffraction, 3 ligands (K70, K, ZN), 3 pockets (best druggability 0.70). MolNFT v1 #137998 on GenesisL1: 3D structure, binding…
- PDB
- 5W5K
- Type
- protein
- Length
- 1,085 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 6
- UniProt
- A7YT55
- Ligands
- K70, K, ZN
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histone deacetylase 6 | protein | 362 | 43% helix, 14% strand | A7YT55 |
| C | Histone deacetylase 6 | protein | 361 | 43% helix, 12% strand | A7YT55 |
Ligands and binding sites
- K70 · 10-{[4-(hydroxycarbamoyl)phenyl]methyl}-5lambda~4~-pyrido[3,2-b][1,4]benzothiazin-10-ium · ligand · 3 copies · chains A, B, C
- K · Potassium ion · metal · 6 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.70 | 0.77 | 78 | ZN, K70 |
| 2 | 269 | 0.48 | 0.73 | 35 | empty |
| 3 | 182 | 0.47 | 0.76 | 32 | empty |
Interfaces
2 interfaces between chains.
- A–B · 443 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 328 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5W5K · Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with… · the same entry in another collection · 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 A7YT55
- Elsewhere: RCSB PDB 5W5K · PDBe 5W5K · UniProt A7YT55
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