Research workbench

HDAC-DC

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

PDB: 6Z6H
Type: protein
Length: 4,774 residues
Chains: 8
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 · 48% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Histone deacetylase HDA1 (EC 3.5.1.98)	protein	651	36% helix, 17% strand	P53973
B, G	Histone deacetylase HDA1 (EC 3.5.1.98)	protein	661	36% helix, 13% strand	P53973
C, I	HDA1 complex subunit 2	protein	541	57% helix, 6% strand	Q06629
D, J	HDA1 complex subunit 3,HDA1 complex subunit 3	protein	534	66% helix, 5% strand	Q06623

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, F, G

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	1177	0.86	0.86	117	empty
2	1144	0.82	0.83	90	empty
3	322	0.81	0.91	42	empty
4	963	0.80	0.82	115	empty
5	86	0.78	0.99	21	empty

Interfaces

16 interfaces between chains.

A–B · 5311 Å² buried · 40 hydrogen bonds · protein-protein
F–G · 5140 Å² buried · 43 hydrogen bonds · protein-protein
F–J · 2029 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 2024 Å² buried · 23 hydrogen bonds · protein-protein
A–D · 2016 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6Z6H · HDAC-DC · the same entry in another collection · chain J against J, TM-score 1.00
P53973 · AlphaFold monomer V2.0 prediction for histone deacetylase HDA1 (P53973) · a predicted model of the same protein · chain F against A, TM-score 0.83

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 6Z6H · PDBe 6Z6H · UniProt P53973 · UniProt Q06629 · UniProt Q06623

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