4X3O: Sirt2

Sirt2 in complex with a myristoyl peptide. Determined by X-ray diffraction at 1.5 Å resolution. Released 13 Jan 2016.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,911
Mol. weight: 35.88 kDa
Ligands: 3Y0, ZN
Released: 13 Jan 2016

Explore 4X3O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4X3O contains 18 α-helices and 17 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, 15 β-strands

Element	Residues	Length	Sheet
α-helix	64-71	8
β-strand	79-83	5	1
α-helix	85-87	3
α-helix	89-91	3
α-helix	103-105	3
α-helix	108-110	3
α-helix	115-119	5
β-strand	120	1	2
α-helix	121-126	6
α-helix	129-138	10
α-helix	147-157	11
β-strand	161-166	6	1
α-helix	172-176	5
α-helix	180-182	3
β-strand	183-185	3	1
β-strand	188-195	8	3
β-strand	203-205	3	3
α-helix	206-215	10
β-strand	220	1	4
β-strand	227	1	4
β-strand	228-232	5	3
β-strand	235	1	2
β-strand	238	1	5
α-helix	239-240	2
α-helix	241-250	10
β-strand	256-260	5	1
β-strand	267	1	6
α-helix	269-275	7
β-strand	282-286	5	1
α-helix	292-294	3
β-strand	317-321	5	1
α-helix	324-335	12
α-helix	338-354	17

Chain C: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	5
β-strand	10	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent protein deacetylase sirtuin-2	A	protein	304	Homo sapiens	Q8IXJ6 (AlphaFold model)
peptide PRO-LYS-LYS-THR-GLY	C	protein	5	Homo sapiens

Sequence of entity 1 (A), FASTA

>4X3O_1 NAD-dependent protein deacetylase sirtuin-2 (chains A)
GSQKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYH
LPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDT
LERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPD
IVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAG
QSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHAS
IDAQ

Sequence of entity 2 (C), FASTA

>4X3O_2 peptide PRO-LYS-LYS-THR-GLY (chains C)
PKKTG

Ligands and cofactors

ID	Name	Formula	Copies
3Y0	[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxid…	C28 H49 N5 O13 P2 S	1
ZN	Zinc ion	Zn	1

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

Primary citation

Deacylation Mechanism by SIRT2 Revealed in the 1'-SH-2'-O-Myristoyl Intermediate Structure. Wang, Y., Fung, Y.M.E., Zhang, W. et al. Cell Chem Biol (2017) 24:339-345. DOI 10.1016/j.chembiol.2017.02.007 · PubMed

Other PDB entries of the same protein (UniProt Q8IXJ6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9S1Z 1.1 Å, Crystal structure of human SIRT2 in complex with the covalent adduct of SirReal-triazole…
9FDR 1.25 Å, Crystal structure of human Sirt2 in apo form with opened selectivity pocket
9FDS 1.4 Å, Crystal structure of human Sirt2 in complex with SirReal2
4RMH 1.42 Å, Human Sirt2 in complex with SirReal2 and Ac-Lys-H3 peptide
30KD 1.45 Å, Crystal structure of human SIRT2 in complex with KMyrMe peptide
4RMI 1.45 Å, Human Sirt2 in complex with SirReal1 and Ac-Lys-OTC peptide
9S46 1.45 Å, Human SIRT2 in Complex with RW-78
9S48 1.45 Å, Human SIRT2 in Complex with RW-80
5YQO 1.48 Å, Crystal structure of Sirt2 in complex with selective inhibitor L5C
9S20 1.5 Å, Crystal structure of human SIRT2 in complex with SirReal-triazole inhibitor SH10
8QOO 1.55 Å, Crystal structure of human Sirt2 in complex with the peptide-based pseudo-inhibitor…
8QT1 1.55 Å, Crystal structure of human Sirt2 in complex with the super-slow substrate TNFn-5

Browse structure collections

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