5D7N: Human Sirt3 at an improved resolution

Crystal structure of human Sirt3 at an improved resolution. Determined by X-ray diffraction at 1.83 Å resolution. Released 2 Dec 2015.

Method: X-ray diffraction
Resolution: 1.83 Å
Organism: Homo sapiens
Chains: 6
Atoms: 14,318
Mol. weight: 189.34 kDa
Ligands: ZN, MG
Released: 2 Dec 2015

Explore 5D7N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D7N contains 129 α-helices and 66 β-strands across 6 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, 11 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	182-185	4
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	265-268	4
α-helix	269-273	5
β-strand	279	1	3
β-strand	286	1	3
β-strand	287-291	5	2
α-helix	292-293	2
α-helix	296-299	4
α-helix	300-304	5
α-helix	305-311	7
β-strand	314-318	5	1
α-helix	328-333	6
β-strand	340-344	5	1
α-helix	349-353	5
β-strand	359-363	5	1
α-helix	366-377	12
α-helix	380-390	11

Chain B: 22 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	125-133	9
β-strand	140-144	5	4
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	4
α-helix	233-236	4
α-helix	241-243	3
β-strand	244-246	3	4
β-strand	249-256	8	5
β-strand	262-264	3	5
α-helix	265-268	4
α-helix	269-273	5
α-helix	276-278	3
β-strand	279	1	6
β-strand	286	1	6
β-strand	287-291	5	5
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	4
α-helix	328-332	5
β-strand	340-344	5	4
α-helix	349-353	5
β-strand	359-363	5	4
α-helix	366-377	12
α-helix	380-391	12

Chain C: 23 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	125-133	9
β-strand	140-144	5	7
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	7
α-helix	233-236	4
α-helix	241-243	3
β-strand	244-246	3	7
β-strand	249-256	8	8
β-strand	262-264	3	8
α-helix	265-268	4
α-helix	269-273	5
α-helix	276-278	3
β-strand	279	1	9
α-helix	285	1
β-strand	286	1	9
β-strand	287-291	5	8
α-helix	292-293	2
α-helix	296-299	4
α-helix	300-304	5
α-helix	305-311	7
β-strand	314-318	5	7
α-helix	327-330	4
β-strand	340-344	5	7
α-helix	350-353	4
β-strand	359-363	5	7
α-helix	366-377	12
α-helix	380-391	12

Chain D: 22 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	125-133	9
β-strand	140-144	5	10
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	182-185	4
α-helix	190-199	10
α-helix	208-218	11
β-strand	222-227	6	10
α-helix	233-236	4
α-helix	241-243	3
β-strand	244-246	3	10
β-strand	249-256	8	11
β-strand	262-264	3	11
α-helix	265-268	4
α-helix	269-273	5
β-strand	279	1	12
α-helix	285	1
β-strand	286	1	12
β-strand	287-291	5	11
α-helix	292-293	2
α-helix	296-299	4
α-helix	300-304	5
α-helix	305-311	7
β-strand	314-318	5	10
α-helix	328-332	5
β-strand	340-344	5	10
α-helix	349-353	5
β-strand	359-363	5	10
α-helix	366-377	12
α-helix	380-391	12

Chain E: 21 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	125-133	9
β-strand	140-144	5	13
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	13
α-helix	233-236	4
α-helix	241-243	3
β-strand	244-246	3	13
β-strand	249-256	8	14
β-strand	262-264	3	14
α-helix	265-268	4
α-helix	269-273	5
β-strand	279	1	15
α-helix	285	1
β-strand	286	1	15
β-strand	287-291	5	14
α-helix	292-293	2
α-helix	296-299	4
α-helix	300-304	5
α-helix	305-311	7
β-strand	314-318	5	13
α-helix	328-332	5
β-strand	340-344	5	13
α-helix	349-353	5
β-strand	359-363	5	13
α-helix	366-377	12
α-helix	380-391	12

Chain F: 21 helices, 11 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
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	17
β-strand	262-264	3	17
α-helix	265-268	4
α-helix	269-273	5
β-strand	279	1	18
β-strand	286	1	18
β-strand	287-291	5	17
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	16
α-helix	328-332	5
β-strand	340-344	5	16
α-helix	349-353	5
β-strand	359-363	5	16
α-helix	366-377	12
α-helix	380-390	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent protein deacetylase sirtuin-3, mitochondrial	A, B, C, D, E, F	protein	281	Homo sapiens	Q9NTG7 (AlphaFold model)

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

>5D7N_1 NAD-dependent protein deacetylase sirtuin-3, mitochondrial (chains A, B, C, D, E, F)
GHMSDKGKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLP
YPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLE
RVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFF
GEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWH
PRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLD

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6
MG	Magnesium ion	Mg	1

Water and common crystallization additives (PEG, 1PE, GOL, PG4, PGE) are not listed.

Primary citation

Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking. Rumpf, T., Gerhardt, S., Einsle, O. et al. Acta Crystallogr F Struct Biol Commun (2015) 71:1498-1510. DOI 10.1107/S2053230X15019986 · 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
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
5Z93 1.95 Å, Crystal Structure of SIRT3 in complex with H3K9bhb peptide

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