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Structure of inhibitor-free HDAC4 catalytic domain (with gain-of-function mutation HIS332TYR)

Analyse Structure of inhibitor-free HDAC4 catalytic domain (with gain-of-function… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VQW
Type: protein
Length: 382 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone deacetylase 4
EC: 3.5.1.98
UniProt: P56524
Ligands: K, ZN
Pockets: 2 · best druggability 0.36

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	Histone deacetylase 4 (EC 3.5.1.98)	protein	382	39% helix, 13% strand	P56524

Ligands and binding sites

K · Potassium ion · metal · 2 copies · chains G
ZN · Zinc ion · metal · 2 copies · chains G

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	72	0.36	0.77	13	empty
2	62	0.35	0.77	17	empty

Compared structures

2VQW · Structure of inhibitor-free HDAC4 catalytic domain (with gain-of- function mutation… · the same entry in another collection · chain G against G, TM-score 1.00
P56524 · AlphaFold monomer V2.0 prediction for histone deacetylase 4 (P56524) · a predicted model of the same protein · chain G 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 P56524
Elsewhere: RCSB PDB 2VQW · PDBe 2VQW · UniProt P56524

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