SMTL ID : 4bvh.3 (2 other biounits)

CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND 2'-O-ACETYL-ADP-RIBOSE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x OCZ: (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide(Non-covalent)

OCZ.1: 13 residues within 4Å: Chain A: S.34, I.39, P.40, F.42, F.65, Q.113, N.114, I.115, D.116, H.133, I.176, V.177 Ligands: OAD.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.39, A:F.42, A:I.115, A:I.115, A:I.115, A:H.133 Hydrogen bonds: A:Q.113, A:I.115, A:D.116, A:D.116 pi-Stacking: A:F.42

1 x OAD: 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE(Non-covalent)

OAD.2: 24 residues within 4Å: Chain A: G.30, A.31, G.32, T.35, P.36, D.41, F.42, R.43, S.44, Y.50, Q.113, H.133, V.177, F.179, G.204, T.205, S.206, V.209, N.229, R.230, G.249, D.250, V.251 Ligands: OCZ.1 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:F.179 Hydrogen bonds: A:A.31, A:T.35, A:D.41, A:D.41, A:F.42, A:R.43, A:R.43, A:Q.113, A:H.133, A:T.205, A:T.205, A:S.206, A:S.206, A:N.229, A:R.230, A:R.230, A:R.230, A:D.250, A:V.251 Water bridges: A:Q.113 Salt bridges: A:R.43, A:R.43, A:H.133 pi-Cation interactions: A:R.230, A:R.230

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 2 residues within 4Å: Chain A: L.16, R.243 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.243, A:R.243 Water bridges: A:D.198 EDO.5: 3 residues within 4Å: Chain A: Q.185, R.186, L.189 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.185 Water bridges: A:R.186 EDO.6: 2 residues within 4Å: Chain A: K.7, D.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.244 Water bridges: A:A.246

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: P.149, D.152 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain A: C.141, C.144, C.165, C.168 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.141, A:C.144, A:C.165, A:C.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gertz, M. et al., Ex-527 Inhibits Sirtuins by Exploiting Their Unique Nad+-Dependent Deacetylation Mechanism. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-07-17

Peptides

NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL

Related Entries With Identical Sequence