Research workbench
Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in complex with acy-1083
Analyse Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WGM
- Type
- protein
- Length
- 1,088 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HDAC6 protein
- UniProt
- A7YT55
- Ligands
- AH7, K, ZN
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HDAC6 protein | protein | 364 | 43% helix, 13% strand | A7YT55 |
| B | HDAC6 protein | protein | 363 | 43% helix, 14% strand | A7YT55 |
| C | HDAC6 protein | protein | 361 | 43% helix, 14% strand | A7YT55 |
Ligands and binding sites
- AH7 · 2-[(4,4-difluoro-1-phenylcyclohexyl)amino]-N-hydroxypyrimidine-5-carboxamide · 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
- EDO · 1,2-ethanediol · additive · 37 copies · chains A, B, C
- PGE · Triethylene glycol · additive · 2 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 489 | 0.70 | 0.80 | 61 | EDO, AH7 |
| 2 | 648 | 0.65 | 0.75 | 82 | PGE, EDO |
| 3 | 162 | 0.39 | 0.72 | 24 | EDO, PEG |
| 4 | 81 | 0.31 | 0.73 | 14 | empty |
Interfaces
2 interfaces between chains.
- B–C · 577 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 338 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5WGM · 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 5WGM · PDBe 5WGM · UniProt A7YT55
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.