MolNFT v1 · #142691 · protein

Histone lysine desuccinylase SIRT5 in complex with succinyl peptide H3K122

6ACE · NAD-dependent protein deacylase sirtuin-5, mitochondrial: “Histone lysine desuccinylase SIRT5 in complex with succinyl peptide H3K122”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.73). MolNFT v1 #142691 on…

PDB: 6ACE
Type: protein
Length: 275 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NAD-dependent protein deacylase sirtuin-5, mitochondrial; Succinyl peptide H3K122
EC: 3.5.1.-
UniProt: Q9NXA8
Ligands: ZN
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NAD-dependent protein deacylase sirtuin-5, mitochondrial (EC 3.5.1.-)	protein	267	37% helix, 19% strand	Q9NXA8
B	Succinyl peptide H3K122	protein	8	0% helix, 25% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · chains A
GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	134	0.73	0.92	28	GOL
2	62	0.33	0.76	17	empty
3	56	0.31	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 617 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (nonstandard).

Compared structures

6ACE · histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122 · the same entry in another collection · chain A against A, TM-score 1.00
Q9NXA8 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacylase sirtuin-5… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9NXA8
Elsewhere: RCSB PDB 6ACE · PDBe 6ACE · UniProt Q9NXA8

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.