Structure of PDB 5d7p Chain B

Receptor sequence

>5d7pB (length=299) Species: 9606 (Homo sapiens)

ERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYD
NLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLL
KDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYP
LSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVD
LLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGG
GMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDA

3D structure

• PDB: 5d7p Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking.
• Chain: B
• Resolution: 1.76 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): P94 D95 F96 R97 N168 D170 H187
• Catalytic site (residue number reindexed from 1): P39 D40 F41 R42 N113 D115 H132
• Enzyme Commision number: 2.3.1.-
  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	ZN	B	C195 C200 C221 C224	C140 C145 C166 C169
BS02	AR6	B	G84 A85 G86 T89 D95 F96 R97 Q167 H187 F235 G261 T262 S263 V266 N286 K287 E288 E323 C324	G29 A30 G31 T34 D40 F41 R42 Q112 H132 F180 G206 T207 S208 V211 N231 K232 E233 E268 C269
BS03	OCZ	B	F131 A135 L138 Y139 G141 D170 F190	F76 A80 L83 Y84 G86 D115 F135	MOAD: ic50=20uM BindingDB: IC50=19600nM
BS04	OCZ	B	F96 F119 Q167 N168 I169 D170 I232 F234	F41 F64 Q112 N113 I114 D115 I177 F179	MOAD: ic50=20uM BindingDB: IC50=19600nM

Gene Ontology

Molecular Function

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

External links

• PDB: RCSB:5d7p, PDBe:5d7p, PDBj:5d7p
• PDBsum: 5d7p
• PubMed: 26625292
• UniProt: Q8IXJ6|SIR2_HUMAN NAD-dependent protein deacetylase sirtuin-2 (Gene Name=SIRT2)