MolNFT v1 · #51381 · protein
Crystal structure of HDAC8-substrate complex
2V5W · Histone deacetylase 8: “Crystal structure of HDAC8-substrate complex”. X-ray diffraction, 4 ligands (ACE, MCM, K), 3 pockets (best druggability 0.83). MolNFT v1 #51381 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2V5W
- Type
- protein
- Length
- 741 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8; Glycyl-glycyl-glycine; Peptidic substrate
- UniProt
- Q9BY41
- Ligands
- ACE, MCM, K, ZN
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 | protein | 363 | 41% helix, 13% strand | Q9BY41 |
| B | Histone deacetylase 8 | protein | 367 | 39% helix, 13% strand | Q9BY41 |
| G | Glycyl-glycyl-glycine | protein | 3 | 0% helix, 0% strand | — |
| I, L | Peptidic substrate | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, I, B, G, L
- MCM · 7-amino-4-methyl-chromen-2-one · ligand · 2 copies · chains A, B, I, L
- K · Potassium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, I, B, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 622 | 0.83 | 0.88 | 82 | MCM |
| 2 | 368 | 0.74 | 0.85 | 51 | empty |
| 3 | 51 | 0.71 | 0.98 | 20 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1051 Ų buried · 8 hydrogen bonds · protein-protein
- B–L · 463 Ų buried · 8 hydrogen bonds · protein-protein
- A–I · 459 Ų buried · 7 hydrogen bonds · protein-protein
- B–G · 178 Ų buried · 4 hydrogen bonds · protein-protein
- A–L · 168 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, acetylation).
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 2V5W · PDBe 2V5W · UniProt Q9BY41
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