Structure of PDB 5y2f Chain A

Receptor sequence

>5y2fA (length=297) Species: 9606 (Homo sapiens) [Search protein sequence]

VNYAAGLSPYADKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTG
AGISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLE
RVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDT
VVGTMGLKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLALADE
ASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADL
RIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPKLEP

3D structure

PDB

5y2f Identification of a cellularly active SIRT6 allosteric activator.

Chain

Resolution

2.53 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	P60 D61 F62 R63 N112 D114 H131
Catalytic site (residue number reindexed from 1)	P60 D61 F62 R63 N112 D114 H131
Enzyme Commision number	2.3.1.- 2.3.1.286: protein acetyllysine N-acetyltransferase. 2.4.2.-

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	peptide	A	D12 W186 E187 D188 S189 L190 I217 R218	D12 W186 E187 D188 S189 L190 I217 R218
BS02	AR6	A	G50 A51 G52 T55 D61 F62 R63 W69 Q111 H131 G212 T213 S214 I217 N238 L239 Q240 Y255 V256	G50 A51 G52 T55 D61 F62 R63 W69 Q111 H131 G212 T213 S214 I217 N238 L239 Q240 Y255 V256
BS03	8L9	A	N2 F80 T83 F84 E85	N2 F80 T83 F84 E85	PDBbind-CN: -logKd/Ki=5.15,Kd=7.0uM BindingDB: EC50=5700nM
BS04	ZN	A	C139 C142 C164 C175	C139 C142 C164 C175
BS05	HDR	A	F84 M155 W186	F84 M155 W186

Gene Ontology

	Molecular Function
GO:0070403	NAD+ binding

View graph for
Molecular Function

External links

PDB	RCSB:5y2f, PDBe:5y2f, PDBj:5y2f
PDBsum	5y2f
PubMed	30374165
UniProt	Q8N6T7\|SIR6_HUMAN NAD-dependent protein deacylase sirtuin-6 (Gene Name=SIRT6)

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