MolNFT v1 · #72128 · protein
Crystal structure of CO2+ HDAC8 complexed with M344
3MZ3 · Histone deacetylase 8: “Crystal structure of CO2+ HDAC8 complexed with M344”. X-ray diffraction, 3 ligands (B3N, K, CO), 6 pockets (best druggability 0.80). MolNFT v1 #72128 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3MZ3
- Type
- protein
- Length
- 713 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8
- EC
- 3.5.1.98
- UniProt
- Q9BY41
- Ligands
- B3N, K, CO
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 (EC 3.5.1.98) | protein | 357 | 39% helix, 13% strand | Q9BY41 |
| B | Histone deacetylase 8 (EC 3.5.1.98) | protein | 356 | 38% helix, 13% strand | Q9BY41 |
Ligands and binding sites
- B3N · 4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.80 | 0.82 | 95 | B3N |
| 2 | 62 | 0.74 | 0.99 | 22 | empty |
| 3 | 60 | 0.72 | 0.98 | 23 | empty |
| 4 | 186 | 0.62 | 0.83 | 41 | empty |
| 5 | 53 | 0.33 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 782 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 Q9BY41
- Elsewhere: RCSB PDB 3MZ3 · PDBe 3MZ3 · UniProt Q9BY41
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