9CBT: Human sirtuin 3 fragment

Crystal structure of human sirtuin 3 fragment (residues 118-399) bound to intermediates from reaction with NAD and inhibitor NH6-10. Determined by X-ray diffraction at 1.95 Å resolution. Released 7 Aug 2024.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,855
Mol. weight: 65.36 kDa
Ligands: 5I7, 5IA, ZN
Released: 7 Aug 2024

Explore 9CBT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CBT contains 40 α-helices and 26 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, 13 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	164-166	3
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
β-strand	279	1	4
α-helix	285	1
β-strand	286	1	4
β-strand	287-291	5	3
β-strand	294	1	2
α-helix	297-299	3
α-helix	300-304	5
α-helix	305-311	7
β-strand	314-318	5	1
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: 20 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	125-133	9
β-strand	140-144	5	5
α-helix	146-148	3
α-helix	150-152	3
α-helix	164-166	3
α-helix	176-180	5
β-strand	181	1	6
α-helix	182-187	6
α-helix	190-198	9
α-helix	208-218	11
β-strand	222-227	6	5
α-helix	233-236	4
α-helix	241-243	3
β-strand	244-246	3	5
β-strand	249-256	8	7
β-strand	262-264	3	7
α-helix	265-267	3
α-helix	269-273	5
β-strand	279	1	8
α-helix	285	1
β-strand	286	1	8
β-strand	287-291	5	7
β-strand	294	1	6
α-helix	297-299	3
α-helix	300-304	5
α-helix	305-311	7
β-strand	314-318	5	5
α-helix	328-332	5
β-strand	340-344	5	5
α-helix	349-353	5
β-strand	359-363	5	5
α-helix	366-377	12
α-helix	380-394	15

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>9CBT_1 NAD-dependent protein deacetylase sirtuin-3, mitochondrial (chains A, B)
SDKGKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPE
AIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVS
GIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEP
LPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRS
RDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLDGPDK

Ligands and cofactors

ID	Name	Formula	Copies
5I7	(phenylmethyl) ~{N}-[(2~{S})-6-[[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-5-[[[[…	C51 H86 N9 O16 P2 S	1
5IA	2-{[(2S)-6-[(Z)-(1-{[(2R,3R,4R,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H…	C51 H86 N9 O16 P2 S	1
ZN	Zinc ion	Zn	2

Water and common crystallization additives (PG4) are not listed.

Primary citation

A Mitochondria-Targeting SIRT3 Inhibitor with Activity against Diffuse Large B Cell Lymphoma. Jana, S., Shang, J., Hong, J.Y. et al. J Med Chem (2024) 67:15428-15437. DOI 10.1021/acs.jmedchem.4c01053 · 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

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