MolNFT v1 · #117626 · protein

Crystal structure of human histone deacetylase 6 catalytic domain 2 in complex with trichostatin a

5EDU · Maltose-binding periplasmic protein, histone deacetylase 6…: “Crystal structure of human histone deacetylase 6 catalytic domain 2 in complex with trichostatin a”. X-ray diffraction, 4 ligands (TSN, GLC, K), 6 pockets (best…

PDB: 5EDU
Type: protein
Length: 1,443 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Maltose-binding periplasmic protein, histone deacetylase 6 chimera
EC: 3.5.1.98
UniProt: P0AEY0, Q9UBN7
Ligands: TSN, GLC, K, ZN
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Maltose-binding periplasmic protein, histone deacetylase 6 chimera (EC 3.5.1.98)	protein	723	42% helix, 17% strand	P0AEY0, Q9UBN7
A	Maltose-binding periplasmic protein, histone deacetylase 6 chimera (EC 3.5.1.98)	protein	720	41% helix, 17% strand	P0AEY0, Q9UBN7

Ligands and binding sites

TSN · Trichostatin A · ligand · 2 copies · chains B, A
GLC · alpha-D-glucopyranose · sugar · 4 copies · chains B, A
K · Potassium ion · metal · 4 copies · chains B, A
ZN · Zinc ion · metal · 2 copies · chains B, A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1174	0.80	0.81	88	GLC
2	1013	0.79	0.81	86	GLC
3	624	0.64	0.74	57	empty
4	72	0.39	0.78	22	empty
5	74	0.38	0.77	19	empty

Interfaces

1 interface between chains.

B–A · 190 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5EDU · Crystal structure of human histone deacetylase 6 catalytic domain 2 in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
Q9UBN7 · AlphaFold monomer V2.0 prediction for histone deacetylase 6 (Q9UBN7) · a predicted model of the same protein · chain A against A, TM-score 0.57

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 P0AEY0
Every structure of UniProt Q9UBN7
Elsewhere: RCSB PDB 5EDU · PDBe 5EDU · UniProt P0AEY0 · UniProt Q9UBN7

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