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Crystal structure analysis of human HDAC8 D101N variant

Analyse Crystal structure analysis of human HDAC8 D101N variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3EZP
Type: protein
Length: 714 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, ZN
Pockets: 3 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Histone deacetylase 8 (EC 3.5.1.98)	protein	357	37% 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
ZN · Zinc ion · metal · 2 copies · chains A, B
BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	764	0.83	0.86	76	ZN, B3N, BME
2	56	0.72	0.99	22	empty
3	50	0.26	0.74	13	empty

Interfaces

1 interface between chains.

A–B · 758 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3EZP · Crystal Structure Analysis of human HDAC8 D101N variant · 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 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 Q9BY41
Elsewhere: RCSB PDB 3EZP · PDBe 3EZP · UniProt Q9BY41

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