8HLY: SIRT3

Crystal structure of SIRT3 in complex with H3K23la peptide. Determined by X-ray diffraction at 2.0 Å resolution. Released 27 Sept 2023.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,370
Mol. weight: 32.37 kDa
Ligands: 2OP, ZN
Released: 27 Sept 2023

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

Secondary structure: helices and β-sheets

8HLY contains 20 α-helices and 17 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: 20 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	125-133	9
β-strand	140-144	5	1
α-helix	146-148	3
α-helix	150-152	3
β-strand	156	1	2
β-strand	159	1	2
α-helix	164-169	6
α-helix	176-180	5
α-helix	182-187	6
α-helix	190-198	9
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	265-267	3
α-helix	269-273	5
β-strand	279	1	4
α-helix	285	1
β-strand	286	1	4
β-strand	287-291	5	3
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
β-strand	324-325	2	6
α-helix	328-332	5
β-strand	340-344	5	1
α-helix	350-353	4
β-strand	359-363	5	1
α-helix	366-377	12
α-helix	380-390	11

Chain B: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	5
β-strand	24-25	2	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent protein deacetylase sirtuin-3, mitochondrial	A	protein	281	Homo sapiens	Q9NTG7 (AlphaFold model)
H3K23la peptide	B	protein	6	Homo sapiens	P68431 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8HLY_1 NAD-dependent protein deacetylase sirtuin-3, mitochondrial (chains A)
DKGKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEA
IFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSG
IPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPL
PQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSR
DVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLDGPDK

Sequence of entity 2 (B), FASTA

>8HLY_2 H3K23la peptide (chains B)
ATKAAR

Ligands and cofactors

ID	Name	Formula	Copies
2OP	(2S)-2-hydroxypropanoic acid	C3 H6 O3	1
ZN	Zinc ion	Zn	1

Water and common crystallization additives (EDO, GOL) are not listed.

Primary citation

Identification of SIRT3 as an eraser of H4K16la. Fan, Z., Liu, Z., Zhang, N. et al. iScience (2023) 26:107757-107757. DOI 10.1016/j.isci.2023.107757 · PubMed

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
8V5U 1.48 Å, Human SIRT3 bound to p53-AMC peptide and Honokiol
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

Browse structure collections

About this viewer

MolViewer shows 8HLY 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.