5Y4H: Human SIRT3

Human SIRT3 in complex with halistanol sulfate. Determined by X-ray diffraction at 2.6 Å resolution. Released 16 May 2018.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,120
Mol. weight: 33.92 kDa
Ligands: 8QF, ZN
Released: 16 May 2018

Explore 5Y4H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Y4H contains 18 α-helices and 13 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: 18 helices, 12 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
α-helix	176-180	5
α-helix	182-187	6
α-helix	190-199	10
α-helix	208-218	11
β-strand	222-227	6	1
α-helix	233-237	5
α-helix	241-243	3
β-strand	244-246	3	1
β-strand	249-256	8	2
β-strand	262-264	3	2
α-helix	269-273	5
α-helix	276-278	3
β-strand	279	1	3
β-strand	286	1	3
β-strand	287-291	5	2
α-helix	297-299	3
α-helix	300-304	5
α-helix	305-308	4
β-strand	314-318	5	1
β-strand	324-325	2	4
α-helix	327-332	6
β-strand	340-343	4	1
α-helix	350-353	4
β-strand	359-361	3	1
α-helix	366-377	12
α-helix	380-387	8

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	6-7	2	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent protein deacetylase sirtuin-3, mitochondrial	A	protein	285	Homo sapiens	Q9NTG7 (AlphaFold model)
Thr-arg-ser-gly-aly-val-met-arg-arg-leu-arg-arg	B	protein	12	Homo sapiens	Q9NUB1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5Y4H_1 NAD-dependent protein deacetylase sirtuin-3, mitochondrial (chains A)
SNASDKGKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLP
YPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLE
RVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFF
GEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWH
PRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLDGPDK

Sequence of entity 2 (B), FASTA

>5Y4H_2 THr-Arg-Ser-GLY-ALY-VAL-MET-ARG-ARG-LEU-ARG-ARG (chains B)
TRSGKVMRRLRR

Ligands and cofactors

ID	Name	Formula	Copies
8QF	[(2~{S},3~{S},5~{S},6~{S},8~{S},9~{S},10~{R},13~{R},14~{R},17~{R})-17-[(2~{R})-…	C28 H50 O12 S3	1
ZN	Zinc ion	Zn	1

Primary citation

Halistanol sulfates I and J, new SIRT1-3 inhibitory steroid sulfates from a marine sponge of the genus Halichondria. Nakamura, F., Kudo, N., Tomachi, Y. et al. J Antibiot (Tokyo) (2018) 71:273-278. DOI 10.1038/ja.2017.145 · 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 5Y4H 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.