5BWO: Human SIRT3

Crystal Structure of Human SIRT3 in Complex with a Palmitoyl H3K9 Peptide. Determined by X-ray diffraction at 2.38 Å resolution. Released 13 Jul 2016.

Method: X-ray diffraction
Resolution: 2.38 Å
Organisms: synthetic construct, Homo sapiens
Chains: 2
Atoms: 2,337
Mol. weight: 35.82 kDa
Ligands: PLM, ZN
Released: 13 Jul 2016

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

Secondary structure: helices and β-sheets

5BWO contains 21 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: 21 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	125-133	9
β-strand	140-144	5	2
α-helix	146-148	3
α-helix	150-152	3
α-helix	165-167	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	2
α-helix	233-236	4
α-helix	241-243	3
β-strand	244-246	3	2
β-strand	249-256	8	3
β-strand	262-264	3	3
α-helix	265-268	4
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
α-helix	292-293	2
α-helix	297-299	3
α-helix	300-304	5
α-helix	305-311	7
β-strand	314-318	5	2
β-strand	324-325	2	1
α-helix	328-332	5
β-strand	340-344	5	2
α-helix	350-353	4
β-strand	359-363	5	2
α-helix	366-377	12
α-helix	380-391	12

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	6-7	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Palmitoyl H3K9 Peptide	B	protein	10	synthetic construct	Q6NXT2 (AlphaFold model)
NAD-dependent protein deacetylase sirtuin-3, mitochondrial	A	protein	309	Homo sapiens	Q9NTG7 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>5BWO_1 Palmitoyl H3K9 Peptide (chains B)
QTARKSTGGW

Sequence of entity 2 (A), FASTA

>5BWO_2 NAD-dependent protein deacetylase sirtuin-3, mitochondrial (chains A)
MASMTGGQQMGRGSHHHHHHENLYFQGSDKGKLSLQDVAELIRARACQRVVVMVGAGIST
PSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTH
YFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRA
DVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASL
TEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRE
TGKLDGPDK

Ligands and cofactors

ID	Name	Formula	Copies
PLM	Palmitic acid	C16 H32 O2	1
ZN	Zinc ion	Zn	1

Primary citation

Crystal structures of SIRT3 reveal that the alpha 2-alpha 3 loop and alpha 3-helix affect the interaction with long-chain acyl lysine. Gai, W., Li, H., Jiang, H. et al. FEBS Lett (2016) 590:3019-3028. DOI 10.1002/1873-3468.12345 · PubMed

Other PDB entries of the same protein (UniProt Q6NXT2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8T4R 1.2 Å, RAG2-PHD finger in complex with H3K4tBuNle peptide
8VLF 1.34 Å, Crystal structure of Ash1L PHD finger in complex with histone H3K4me3
2PUY 1.43 Å, Crystal Structure of the BHC80 PHD finger
9C0O 1.53 Å, Crystal structure of DmCfp1 PHD finger bound to H3K4me3
6OI3 1.66 Å, Crystal structure of human WDR5 in complex with monomethyl H3R2 peptide
9DZN 1.72 Å, KAT6A MYST domain complexed with a H3K14-CoA bisubstrate inhibitor
7TRL 1.74 Å, Crystal structure of human BIRC2 BIR3 domain in complex with histone H3
8VLD 1.92 Å, Crystal structure of Ash1L PHD finger in complex with histone H3K4me2
5BWN 1.94 Å, Crystal Structure of SIRT3 with a H3K9 Peptide Containing a Myristoyl Lysine
9V5M 2.1 Å, The crystal structure of RBBP4-H3 complex
3KV4 2.19 Å, Structure of PHF8 in complex with histone H3
7W67 2.19 Å, The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with…

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