SMTL ID : 4bvh.2 (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: 14 residues within 4Å: Chain A: S.34, I.39, P.40, F.42, F.65, L.84, Q.113, N.114, I.115, D.116, H.133, I.176, V.177 Ligands: AR6.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.39, A:F.42, A:L.84, 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, A:D.116 pi-Stacking: A:F.42, A:F.65

1 x AR6: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE(Non-covalent)

AR6.2: 23 residues within 4Å: Chain A: G.30, A.31, G.32, T.35, D.41, F.42, R.43, S.44, Y.50, Q.113, H.133, F.179, G.204, T.205, S.206, V.209, N.229, R.230, D.231, G.249, D.250, V.251 Ligands: OCZ.1 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:A.31, A:T.35, A:F.42, A:R.43, A:R.43, A:Y.50, A:Y.50, A:Q.113, A:S.206, A:S.206, A:L.207, A:N.229, A:R.230, A:R.230, A:R.230, A:D.231, A:D.250, A:D.250, A:V.251 Salt bridges: A:R.43, A:R.43 pi-Cation interactions: A:R.230, A:R.230

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

EDO.3: 3 residues within 4Å: Chain A: P.195, A.197, R.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.197 Water bridges: A:A.197, A:R.220 EDO.4: 2 residues within 4Å: Chain A: V.121, E.275 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.275, A:E.275 Water bridges: A:Y.96

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: C.141, V.143, 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

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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
B

NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL

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