MolNFT v1 · #123063 · protein

A histone deacetylase from saccharomyces cerevisiae

5J8J · Histone deacetylase HDA1: “A histone deacetylase from saccharomyces cerevisiae”. X-ray diffraction, 3 pockets (best druggability 0.47). MolNFT v1 #123063 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5J8J
Type: protein
Length: 244 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone deacetylase HDA1
EC: 3.5.1.98
UniProt: P53973
Pockets: 3 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone deacetylase HDA1 (EC 3.5.1.98)	protein	244	39% helix, 20% strand	P53973

Pockets

3 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	101	0.47	0.80	22	empty
2	60	0.34	0.77	17	empty
3	51	0.26	0.73	10	empty

Compared structures

5J8J · A histone deacetylase from Saccharomyces cerevisiae · the same entry in another collection · chain A against A, TM-score 1.00
P53973 · AlphaFold monomer V2.0 prediction for histone deacetylase HDA1 (P53973) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P53973
Elsewhere: RCSB PDB 5J8J · PDBe 5J8J · UniProt P53973

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