5YTK: SIRT3

Crystal structure of SIRT3 bound to a leucylated AceCS2. Determined by X-ray diffraction at 2.7 Å resolution. Released 27 Dec 2017.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 10
Atoms: 13,332
Mol. weight: 188.19 kDa
Ligands: LYS, LEU, ZN
Released: 27 Dec 2017

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

Secondary structure: helices and β-sheets

5YTK contains 125 α-helices and 78 β-strands across 10 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, 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	163-168	6
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	233-236	4
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	266-273	8
α-helix	276-278	3
β-strand	279	1	3
β-strand	286	1	3
β-strand	287-291	5	2
α-helix	292-293	2
β-strand	297	1	4
α-helix	298-299	2
α-helix	300-304	5
α-helix	305-311	7
β-strand	314-318	5	1
α-helix	327-330	4
β-strand	340-344	5	1
α-helix	350-353	4
β-strand	359-363	5	1
α-helix	366-377	12
α-helix	380-393	14

Chain B: 20 helices, 11 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	163-169	7
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	5
α-helix	233-236	4
α-helix	241-243	3
β-strand	244-246	3	5
β-strand	249-256	8	6
β-strand	262-264	3	6
α-helix	266-273	8
α-helix	276-278	3
β-strand	279	1	7
β-strand	286	1	7
β-strand	287-291	5	6
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	5
α-helix	327-330	4
β-strand	340-344	5	5
α-helix	350-353	4
β-strand	359-363	5	5
α-helix	366-377	12
α-helix	380-393	14

Chain C: 21 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	125-133	9
β-strand	140-144	5	8
α-helix	146-148	3
α-helix	150-152	3
α-helix	154-156	3
α-helix	163-169	7
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	8
α-helix	233-236	4
α-helix	241-243	3
β-strand	244-246	3	8
β-strand	249-256	8	9
β-strand	262-264	3	9
α-helix	266-273	8
β-strand	279	1	10
α-helix	285	1
β-strand	286	1	10
β-strand	287-291	5	9
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	8
α-helix	328-332	5
β-strand	340-344	5	8
α-helix	350-353	4
β-strand	359-363	5	8
α-helix	366-377	12
α-helix	380-393	14

Chain D: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	125-133	9
β-strand	140-144	5	11
α-helix	146-152	7
β-strand	160	1	12
β-strand	162	1	12
α-helix	163-168	6
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	11
α-helix	233-236	4
α-helix	241-243	3
β-strand	244-246	3	11
β-strand	249-256	8	13
β-strand	262-264	3	13
α-helix	266-273	8
α-helix	276-278	3
β-strand	279	1	14
β-strand	286	1	14
β-strand	287-291	5	13
α-helix	292-293	2
β-strand	297	1	15
α-helix	298-299	2
α-helix	300-304	5
α-helix	305-311	7
β-strand	314-318	5	11
α-helix	327-330	4
β-strand	340-344	5	11
α-helix	350-353	4
β-strand	359-363	5	11
α-helix	366-377	12
α-helix	380-393	14

Chain E: 21 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	125-133	9
β-strand	140-144	5	16
α-helix	146-148	3
α-helix	150-152	3
α-helix	154-156	3
β-strand	160	1	17
β-strand	162	1	17
α-helix	163-169	7
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	16
α-helix	233-236	4
α-helix	241-243	3
β-strand	244-246	3	16
β-strand	249-256	8	18
β-strand	262-264	3	18
α-helix	266-273	8
α-helix	276-278	3
β-strand	279	1	19
β-strand	286	1	19
β-strand	287-291	5	18
α-helix	292-293	2
β-strand	297	1	20
α-helix	298-299	2
α-helix	300-304	5
α-helix	305-311	7
β-strand	314-318	5	16
α-helix	327-330	4
β-strand	340-343	4	16
α-helix	350-353	4
β-strand	359-361	3	16
α-helix	366-377	12
α-helix	380-393	14

Chain F: 22 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	125-133	9
β-strand	140-144	5	21
α-helix	146-148	3
α-helix	150-152	3
α-helix	154-156	3
α-helix	163-168	6
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	21
α-helix	233-236	4
α-helix	241-243	3
β-strand	244-246	3	21
β-strand	249-256	8	22
β-strand	262-264	3	22
α-helix	265-268	4
α-helix	269-273	5
α-helix	276-278	3
β-strand	279	1	23
β-strand	286	1	23
β-strand	287-291	5	22
α-helix	292-293	2
β-strand	297	1	24
α-helix	298-299	2
α-helix	300-304	5
α-helix	305-311	7
β-strand	314-318	5	21
α-helix	327-330	4
β-strand	340-344	5	21
α-helix	350-353	4
β-strand	359-363	5	21
α-helix	366-377	12
α-helix	380-393	14

Chains G, J and L: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	643	1	4

Chain K: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	642	1
β-strand	643	1	20
α-helix	644	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent protein deacetylase sirtuin-3, mitochondrial	A, B, C, D, E, F	protein	274	Homo sapiens	Q9NTG7 (AlphaFold model)
AceCS2-KLeu	G, J, K, L	protein	8	Homo sapiens	Q9NUB1 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>5YTK_1 NAD-dependent protein deacetylase sirtuin-3, mitochondrial (chains A, B, C, D, E, F)
GKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIF
ELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIP
ASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQ
RFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDV
AQLGDVVHGVESLVELLGWTEEMRDLVQRETGKL

Sequence of entity 2 (G, J, K, L), FASTA

>5YTK_2 AceCS2-KLeu (chains G, J, K, L)
TRSGKVMR

Ligands and cofactors

ID	Name	Formula	Copies
LYS	Lysine	C6 H15 N2 O2	2
LEU	Leucine	C6 H13 N O2	6
ZN	Zinc ion	Zn	6

Primary citation

Sensing and Transmitting Intracellular Amino Acid Signals through Reversible Lysine Aminoacylations. He, X.D., Gong, W., Zhang, J.N. et al. Cell Metab (2018) 27:151-166.e6. DOI 10.1016/j.cmet.2017.10.015 · 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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