SMTL ID : 4bv3.1

CRYSTAL STRUCTURE OF SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Covalent)

NAD.1: 26 residues within 4Å: Chain A: G.30, A.31, G.32, T.35, D.41, F.42, R.43, Y.50, F.65, Q.113, H.133, V.177, F.179, G.204, T.205, S.206, V.209, N.229, R.230, D.231, G.249, D.250, V.251 Ligands: APR.2, OCZ.3, GOL.6 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:F.65 Hydrogen bonds: A:A.31, A:G.32, A:T.35, A:F.42, A:R.43, A:Y.50, A:Q.113, A:V.177, A:S.206, A:S.206, A:N.229, A:R.230, A:R.230, A:D.250, A:D.250, A:V.251 Water bridges: A:S.44, A:L.207, A:L.207, A:D.231 Salt bridges: A:R.43 pi-Stacking: A:F.179 pi-Cation interactions: A:R.230

1 x APR: ADENOSINE-5-DIPHOSPHORIBOSE(Non-covalent)

APR.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, G.249, D.250, V.251 Ligands: NAD.1, OCZ.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:A.31, A:G.32, A:T.35, A:F.42, A:R.43, A:Y.50, A:S.206, A:S.206, A:N.229, A:R.230, A:R.230, A:D.250, A:D.250, A:V.251 Water bridges: A:S.44, A:L.207, A:L.207, A:D.231 Salt bridges: A:R.43, A:R.43 pi-Cation interactions: A:R.230

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

OCZ.3: 17 residues within 4Å: Chain A: A.31, I.39, P.40, F.42, L.49, F.65, L.84, Q.113, N.114, I.115, D.116, H.133, I.176, V.177, F.178 Ligands: NAD.1, APR.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.31, A:I.39, A:L.49, A:L.84, A:I.115, A:I.115, A:H.133, A:I.176 Hydrogen bonds: A:Q.113, A:I.115, A:D.116, A:D.116 pi-Stacking: A:F.42, A:F.65

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 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

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.5: 8 residues within 4Å: Chain A: H.133, L.183, F.187, V.209, E.210, P.211, F.212 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.209, A:F.212

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain A: H.133, V.177, F.178, F.179, G.180, E.181, L.183 Ligands: NAD.1, NO3.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.133, A:G.180, A:G.180 GOL.7: 3 residues within 4Å: Chain A: P.36, K.90, N.92 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 4 residues within 4Å: Chain A: E.210, A.213, S.214, P.235 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.210

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

CL.9: 3 residues within 4Å: Chain A: G.234, P.235, W.238 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
A

NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL

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