Structure of PDB 3riy Chain B

Receptor sequence

>3riyB (length=272) Species: 9606 (Homo sapiens)

SFTARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKW
QAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGK
QGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPI
CPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPA
ILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTP
ATNRFRFHFQGPCGTTLPEALA

3D structure

• PDB: 3riy Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase
• Chain: B
• Resolution: 1.55 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): P68 T69 F70 R71 N141 D143 H158
• Catalytic site (residue number reindexed from 1): P38 T39 F40 R41 N111 D113 H128
• Enzyme Commision number: 2.3.1.-

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	B	Q83 Y102 R105 I142 H158 V221 W222 F223 G224 E225 N226 L227 L232 V253 V254 Y255 P256	Q53 Y72 R75 I112 H128 V191 W192 F193 G194 E195 N196 L197 L202 V223 V224 Y225 P226
BS02	ZN	B	C166 C169 C207 C212	C136 C139 C177 C182
BS03	NAD	B	A59 G60 E64 P68 T69 F70 R71 Q140 N141 D143 G249 T250 S251 N275 T276 E277 P292 C293	A29 G30 E34 P38 T39 F40 R41 Q110 N111 D113 G219 T220 S221 N245 T246 E247 P262 C263

Gene Ontology

Molecular Function

• GO:0036054 protein-malonyllysine demalonylase activity
• GO:0036055 protein-succinyllysine desuccinylase activity
• GO:0070403 NAD+ binding

External links

• PDB: RCSB:3riy, PDBe:3riy, PDBj:3riy
• PDBsum: 3riy
• PubMed: 22076378
• UniProt: Q9NXA8|SIR5_HUMAN NAD-dependent protein deacylase sirtuin-5, mitochondrial (Gene Name=SIRT5)