Research workbench
Crystal structure of danio rerio histone deacetylase 6 catalytic domain 1 in complex with trichostatin a
Analyse Crystal structure of danio rerio histone deacetylase 6 catalytic domain 1 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EEF
- Type
- protein
- Length
- 714 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HDAC6
- UniProt
- F8W4B7
- Ligands
- TSN, ZN, NH4, SO4
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HDAC6 | protein | 354 | 43% helix, 13% strand | F8W4B7 |
| B | HDAC6 | protein | 360 | 45% helix, 14% strand | F8W4B7 |
Ligands and binding sites
- TSN · Trichostatin A · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NH4 · Ammonium ion · ion · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
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 | 84 | 0.67 | 0.92 | 21 | empty |
| 2 | 220 | 0.58 | 0.80 | 46 | SO4, EDO |
| 3 | 77 | 0.57 | 0.88 | 17 | EDO |
| 4 | 71 | 0.45 | 0.81 | 17 | TSN |
| 5 | 53 | 0.38 | 0.80 | 18 | TSN |
Interfaces
1 interface between chains.
- A–B · 1636 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5EEF · Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 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 F8W4B7
- Elsewhere: RCSB PDB 5EEF · PDBe 5EEF · UniProt F8W4B7
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