SMTL ID : 4bvg.1

CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH NATIVE ALKYLIMIDATE FORMED FROM ACETYL-LYSINE ACS2-PEPTIDE CRYSTALLIZED IN PRESENCE OF THE INHIBITOR EX-527

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: V.143, C.144, Q.145 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.143 EDO.2: 7 residues within 4Å: Chain A: Y.85, P.86, F.136, A.137, G.150, E.151, R.154 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.85, A:R.154 Water bridges: A:T.135, A:T.135 EDO.3: 1 residues within 4Å: Chain A: H.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.72 EDO.4: 8 residues within 4Å: Chain A: N.114, I.115, D.116, G.117, E.131, G.134, T.135, F.136 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.115, A:G.117, A:E.131, A:T.135, A:F.136 Water bridges: A:E.119 EDO.8: 4 residues within 4Å: Chain A: S.37, N.88, Y.89, K.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.90, A:K.90 EDO.9: 6 residues within 4Å: Chain A: Q.23, R.24, G.105, L.106, L.107, K.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.105, A:K.128 EDO.12: 2 residues within 4Å: Chain A: R.269, Q.273 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.273

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: K.75, V.162, R.164 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.162, A:R.164, A:R.164 GOL.6: 8 residues within 4Å: Chain A: A.31, S.34, I.39, P.40, F.42, N.114, I.115, D.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.39, A:I.115 GOL.7: 1 residues within 4Å: Chain A: C.144 No protein-ligand interaction detected (PLIP)

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 4 residues within 4Å: Chain A: R.230, G.249, D.250, H.253 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.230, A:D.250 Salt bridges: A:H.253 SO4.11: 3 residues within 4Å: Chain A: R.109, S.127, R.186 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.109, A:R.186

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 6 residues within 4Å: Chain A: R.43, S.44, P.45, R.230, D.231 Ligands: XYQ.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.43, A:R.230

1 x ZN: ZINC ION(Non-covalent)

ZN.14: 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 XYQ: (2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL ACETATE(Non-covalent)

XYQ.15: 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, I.176, V.177, F.179, G.204, T.205, S.206, V.209, N.229, R.230, D.231, G.249, D.250, V.251 Chain B: K.5 Ligands: PEG.13 25 PLIP interactions: 24 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.65, A:I.176 Hydrogen bonds: A:A.31, A:G.32, A:T.35, A:D.41, A:F.42, A:R.43, A:R.43, A:R.43, A:Y.50, A:T.205, A:S.206, A:S.206, A:L.207, A:N.229, A:R.230, A:D.250, A:V.251 Water bridges: A:H.133, A:H.133 Salt bridges: A:R.43, A:H.133, B:K.5 pi-Cation interactions: A:R.230

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. U.S.A. (2013)

Release Date

2013-07-17

Peptides

NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL: A
ACETYL-COENZYME A SYNTHETASE 2-LIKE, MITOCHONDRIAL: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL

ACETYL-COENZYME A SYNTHETASE 2-LIKE, MITOCHONDRIAL

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