MolNFT v1 · #92058 · protein

Human SIRT3 bound to ac-acs peptide and carba-NAD

4FVT · NAD-dependent protein deacetylase sirtuin-3, mitochondrial: “Human SIRT3 bound to ac-acs peptide and carba-NAD”. X-ray diffraction, 3 ligands (CNA, ZN, SO4), 3 pockets (best druggability 0.75). MolNFT v1 #92058 on GenesisL1: 3D…

PDB: 4FVT
Type: protein
Length: 279 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NAD-dependent protein deacetylase sirtuin-3, mitochondrial; Acetylated ACS2 peptide
EC: 3.5.1.-
UniProt: Q9NTG7
Ligands: CNA, ZN, SO4
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-)	protein	274	43% helix, 18% strand	Q9NTG7
B	Acetylated ACS2 peptide	protein	5	0% helix, 40% strand	—

Ligands and binding sites

CNA · Carba-nicotinamide-adenine-dinucleotide · ligand · chains A, B
ZN · Zinc ion · metal · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A
GOL · Glycerol · additive · 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	433	0.75	0.84	41	CNA
2	75	0.35	0.76	17	empty
3	60	0.26	0.73	22	empty

Interfaces

1 interface between chains.

A–B · 436 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (acetylation, nonstandard).

Compared structures

4FVT · Human SIRT3 bound to Ac-ACS peptide and Carba-NAD · the same entry in another collection · chain A against A, TM-score 1.00
Q9NTG7 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase sirtuin-3… · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q9NTG7
Elsewhere: RCSB PDB 4FVT · PDBe 4FVT · UniProt Q9NTG7

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