8V5U: Human SIRT3

Human SIRT3 bound to p53-AMC peptide and Honokiol. Determined by X-ray diffraction at 1.48 Å resolution. Released 6 Nov 2024.

Method: X-ray diffraction
Resolution: 1.48 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,299
Mol. weight: 32.37 kDa
Ligands: ZN, Y4T
Released: 6 Nov 2024

Explore 8V5U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8V5U contains 22 α-helices and 15 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 22 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	122-124	3
α-helix	125-133	9
β-strand	140-144	5	1
α-helix	146-148	3
α-helix	150-152	3
α-helix	164-167	4
α-helix	176-180	5
β-strand	181	1	2
α-helix	182-187	6
α-helix	190-199	10
α-helix	208-218	11
β-strand	222-227	6	1
α-helix	233-236	4
α-helix	241-243	3
β-strand	244-246	3	1
β-strand	249-256	8	3
β-strand	262-264	3	3
α-helix	265-268	4
α-helix	269-273	5
α-helix	276-278	3
β-strand	279	1	4
β-strand	286	1	4
β-strand	287-291	5	3
α-helix	292-293	2
β-strand	294	1	2
β-strand	297	1	5
α-helix	298-299	2
α-helix	300-304	5
α-helix	305-311	7
β-strand	314-318	5	1
α-helix	327-333	7
β-strand	340-344	5	1
α-helix	349-353	5
β-strand	359-363	5	1
α-helix	366-377	12
α-helix	380-391	12

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent protein deacetylase sirtuin-3, mitochondrial	A	protein	282	Homo sapiens	Q9NTG7 (AlphaFold model)
p53-AMC peptide	B	protein	5	Homo sapiens

Sequence of entity 1 (A), FASTA

>8V5U_1 NAD-dependent protein deacetylase sirtuin-3, mitochondrial (chains A)
SDKGKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPE
AIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVS
GIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEP
LPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRS
RDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLDGPDK

Sequence of entity 2 (B), FASTA

>8V5U_2 p53-AMC peptide (chains B)
QPKKX

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
Y4T	(1P)-3',5-di(prop-2-en-1-yl)[1,1'-biphenyl]-2,4'-diol	C18 H18 O2	1

Primary citation

Computationally Driven Discovery and Characterization of SIRT3-Activating Compounds that Fully Recover Catalytic Activity under ${\mathrm{NAD}}^{+}$ Depletion. Guan, X., Dumpati, R.K., Munshi, S. et al. Phys Rev X (2024) 14. DOI 10.1103/PhysRevX.14.041019

Other PDB entries of the same protein (UniProt Q9NTG7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8ANC 1.11 Å, 14-3-3 sigma sirtuin-3 phospho-peptide complex
4BN4 1.3 Å, Structure of human SIRT3 in complex with ADP-ribose
9S27 1.6 Å, Crystal structure of human SIRT3 in complex with the covalent adduct of peptide triazole…
8CCW 1.65 Å, Crystal structure of human Sirt3 in complex with an acetylated HIV1 Tat-46-54 substrate…
4JSR 1.7 Å, Crystal Structure of human SIRT3 with ELT inhibitor 11c…
8V2N 1.74 Å, Human SIRT3 co-crystallized with ligands, including p53-AMC peptide and Carba-NAD
3GLR 1.8 Å, Crystal Structure of human SIRT3 with acetyl-lysine AceCS2 peptide
5D7N 1.83 Å, Crystal structure of human Sirt3 at an improved resolution
5Z94 1.9 Å, Crystal Structure of SIRT3 in complex with H3K4bhb peptide
4BVH 1.9 Å, Crystal structure of human SIRT3 in complex with the inhibitor ex-527 and…
5BWN 1.94 Å, Crystal Structure of SIRT3 with a H3K9 Peptide Containing a Myristoyl Lysine
5Z93 1.95 Å, Crystal Structure of SIRT3 in complex with H3K9bhb peptide

Browse structure collections

About this viewer

MolViewer shows 8V5U directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.