MolNFT v1 · #63132 · protein
Crystal structure analysis of human HDAC8 complexed with apha in a new monoclinic crystal form
3F07 · Histone deacetylase 8: “Crystal structure analysis of human HDAC8 complexed with apha in a new monoclinic crystal form”. X-ray diffraction, 3 ligands (AGE, K, ZN), 5 pockets (best druggability 0.74). MolNFT v1 #63132 on GenesisL1…
- PDB
- 3F07
- Type
- protein
- Length
- 1,074 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 8
- EC
- 3.5.1.98
- UniProt
- Q9BY41
- Ligands
- AGE, K, ZN
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 8 (EC 3.5.1.98) | protein | 366 | 40% helix, 13% strand | Q9BY41 |
| B | Histone deacetylase 8 (EC 3.5.1.98) | protein | 368 | 41% helix, 13% strand | Q9BY41 |
| C | Histone deacetylase 8 (EC 3.5.1.98) | protein | 340 | 41% helix, 14% strand | Q9BY41 |
Ligands and binding sites
- AGE · (2E)-N-hydroxy-3-[1-methyl-4-(phenylacetyl)-1H-pyrrol-2-yl]prop-2-enamide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 6 copies · chains A, B, C
- ZN · Zinc ion · metal · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.74 | 0.82 | 57 | empty |
| 2 | 51 | 0.72 | 0.99 | 19 | empty |
| 3 | 50 | 0.70 | 0.98 | 19 | empty |
| 4 | 217 | 0.56 | 0.78 | 33 | AGE |
| 5 | 56 | 0.40 | 0.81 | 21 | ZN, AGE |
Interfaces
2 interfaces between chains.
- B–C · 689 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3F07 · Crystal Structure Analysis of Human HDAC8 complexed with APHA in a new monoclinic crystal… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BY41 · AlphaFold monomer V2.0 prediction for histone deacetylase 8 (Q9BY41) · a predicted model of the same protein · chain C 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 Q9BY41
- Elsewhere: RCSB PDB 3F07 · PDBe 3F07 · UniProt Q9BY41
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