MolNFT v1 · #138355 · protein
Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in complex with acy-1083
5WGM: “Crystal structure of danio rerio histone deacetylase 6 catalytic domain 2 in complex with acy-1083”. X-ray diffraction, 3 ligands (AH7, K, ZN). MolNFT v1 #138355 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WGM
- Type
- protein
- Length
- 1,088 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- A7YT55
- Ligands
- AH7, K, ZN
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 364 | — | A7YT55 |
| B | — | protein | 363 | — | A7YT55 |
| C | — | protein | 361 | — | 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.
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
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