Research workbench

HDAC-TC

Analyse HDAC-TC in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Z6O
Type: protein
Length: 9,628 residues
Chains: 16
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone deacetylase HDA1; HDA1 complex subunit 2; HDA1 complex subunit 3,HDA1 complex…
EC: 3.5.1.98
UniProt: P53973, Q06629, Q06623
Ligands: ZN
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 4 distinct chains · 46% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, I, M	Histone deacetylase HDA1 (EC 3.5.1.98)	protein	656	36% helix, 15% strand	P53973
B, F, J, N	Histone deacetylase HDA1 (EC 3.5.1.98)	protein	661	35% helix, 15% strand	P53973
C, G, K, O	HDA1 complex subunit 2	protein	548	55% helix, 6% strand	Q06629
D, H, L, P	HDA1 complex subunit 3,HDA1 complex subunit 3	protein	542	63% helix, 6% strand	Q06623

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, E, F, I, J, M, N

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	909	0.86	0.87	132	empty
2	956	0.86	0.87	136	empty
3	1163	0.84	0.85	142	empty
4	1120	0.81	0.82	101	empty
5	532	0.81	0.87	67	empty

Interfaces

36 interfaces between chains.

E–F · 5465 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 5460 Å² buried · 38 hydrogen bonds · protein-protein
M–N · 5454 Å² buried · 38 hydrogen bonds · protein-protein
I–J · 5444 Å² buried · 37 hydrogen bonds · protein-protein
J–K · 2506 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6Z6O · HDAC-TC · the same entry in another collection · chain K against K, 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 P53973
Every structure of UniProt Q06629
Every structure of UniProt Q06623
Elsewhere: RCSB PDB 6Z6O · PDBe 6Z6O · UniProt P53973 · UniProt Q06629 · UniProt Q06623

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