Structure of PDB 5h4d Chain A

Receptor sequence

>5h4dA (length=271) Species: 9606 (Homo sapiens)

GKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQ
YDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKG
LLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRA
DVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGT
SLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGV
ESLVELLGWTEEMRDLVQRET

3D structure

• PDB: 5h4d Crystal structure of hSIRT3 in complex with a specific agonist Amiodarone hydrochloride
• Chain: A
• Resolution: 3.21 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): P155 D156 F157 R158 N229 D231 H248
• Catalytic site (residue number reindexed from 1): P35 D36 F37 R38 N109 D111 H128
• Enzyme Commision number: 2.3.1.286: protein acetyllysine N-acetyltransferase.

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	F180 H248 V292 F294 G295 E296 P297 L298 F302 P326	F60 H128 V172 F174 G175 E176 P177 L178 F182 P206
BS02	ZN	A	C256 C259 C280 C283	C136 C139 C160 C163
BS03	BBI	A	F157 R158 E177 F294	F37 R38 E57 F174
BS04	NAD	A	G145 A146 G147 S149 T150 F157 Q228 N229 I230 D231 H248 G319 T320 S321 D365 V366	G25 A26 G27 S29 T30 F37 Q108 N109 I110 D111 H128 G199 T200 S201 D245 V246

Gene Ontology

Molecular Function

• GO:0017136 NAD-dependent histone deacetylase activity
• GO:0051287 NAD binding
• GO:0070403 NAD+ binding

External links

• PDB: RCSB:5h4d, PDBe:5h4d, PDBj:5h4d
• PDBsum: 5h4d
• UniProt: Q9NTG7|SIR3_HUMAN NAD-dependent protein deacetylase sirtuin-3, mitochondrial (Gene Name=SIRT3)