Structure of PDB 5d7q Chain B

Receptor sequence

>5d7qB (length=300) Species: 9606 (Homo sapiens)

ERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYD
NLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLL
KDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYP
LSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVD
LLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGG
GMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ

3D structure

• PDB: 5d7q Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking.
• Chain: B
• Resolution: 2.01 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 Y104 Q167 H187 F235 G261 T262 S263 V266 N286 K287 E288 E323 C324	G29 A30 G31 T34 D40 F41 R42 Y49 Q112 H132 F180 G206 T207 S208 V211 N231 K232 E233 E268 C269
BS03	4I5	B	P94 F96 Q167 N168 I169 D170 I232 F234	P39 F41 Q112 N113 I114 D115 I177 F179	MOAD: ic50=2.8uM BindingDB: IC50=2770nM
BS04	4I5	B	I93 A135 L138 Y139 G141 D170 F190	I38 A80 L83 Y84 G86 D115 F135	MOAD: ic50=2.8uM BindingDB: IC50=2770nM

Gene Ontology

Molecular Function

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

External links

• PDB: RCSB:5d7q, PDBe:5d7q, PDBj:5d7q
• PDBsum: 5d7q
• PubMed: 26625292
• UniProt: Q8IXJ6|SIR2_HUMAN NAD-dependent protein deacetylase sirtuin-2 (Gene Name=SIRT2)