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Crystal structure of ligand-free danio rerio HDAC6 CD1 CD2

Analyse Crystal structure of ligand-free danio rerio HDAC6 CD1 CD2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7QNO
Type: protein
Length: 755 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone deacetylase 6
UniProt: F8W4B7
Ligands: PRO, K, ZN
Pockets: 5 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone deacetylase 6	protein	755	42% helix, 12% strand	F8W4B7

Ligands and binding sites

PRO · Proline · ligand · chains A
K · Potassium ion · metal · 4 copies · chains A
ZN · Zinc ion · metal · chains A
GOL · Glycerol · additive · 6 copies · chains A

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

Pockets

5 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	126	0.59	0.85	31	empty
2	72	0.51	0.85	17	empty
3	206	0.47	0.75	28	empty
4	115	0.45	0.78	25	empty
5	50	0.33	0.77	11	empty

Compared structures

7QNO · Crystal structure of ligand-free Danio rerio HDAC6 CD1 CD2 · the same entry in another collection · 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 F8W4B7
Elsewhere: RCSB PDB 7QNO · PDBe 7QNO · UniProt F8W4B7

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