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Crystal structure of danio rerio histone deacetylase 6 catalytic domain 1 (CD1) complexed with trichostatin a

Analyse Crystal structure of danio rerio histone deacetylase 6 catalytic domain 1 (CD1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UO2
Type: protein
Length: 714 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HDAC6
UniProt: F8W4B7
Ligands: TSN, K, ZN
Pockets: 1 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	HDAC6	protein	357	44% helix, 13% strand	F8W4B7

Ligands and binding sites

TSN · Trichostatin A · ligand · 2 copies · chains A, B
K · Potassium ion · metal · 4 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1185	0.80	0.81	116	TSN

Interfaces

1 interface between chains.

A–B · 395 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6UO2 · Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) complexed… · the same entry in another collection · chain B against B, 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 F8W4B7
Elsewhere: RCSB PDB 6UO2 · PDBe 6UO2 · UniProt F8W4B7

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