SMTL ID : 4x3o.1

Sirt2 in complex with a myristoyl peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x PRO- LYS- LYS- THR- GLY: peptide PRO-LYS-LYS-THR-GLY(Non-covalent)

PRO-LYS-LYS-THR-GLY.1: 14 residues within 4Å: Chain A: H.136, V.182, F.183, F.184, G.185, E.186, S.187, L.188, F.193, Q.214, V.215, Q.216, P.217 Ligands: 3Y0.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.182, A:F.184, A:L.188, A:F.193, A:V.215 Hydrogen bonds: A:V.182, A:G.185, A:E.186, A:L.188, A:Q.216, A:Q.216 Water bridges: A:L.188

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.144, C.149, C.170, C.173 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.144, A:C.149, A:C.170, A:C.173

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

EDO.3: 3 residues within 4Å: Chain A: L.284, G.285, W.286 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.289, A:E.289 EDO.4: 3 residues within 4Å: Chain A: A.268, W.269, L.270 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.268, A:L.270 Water bridges: A:L.270

1 x 3Y0: [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4R,5R)-3-oxidanyl-5-sulfanyl-4-tridecoxy-oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

3Y0.5: 29 residues within 4Å: Chain A: G.33, A.34, G.35, T.38, D.44, F.45, R.46, S.47, Y.53, F.68, F.80, Y.88, Q.116, I.118, H.136, F.139, V.182, F.184, G.210, T.211, S.212, V.215, N.235, K.236, E.237, G.271, E.272, C.273 Ligands: PRO-LYS-LYS-THR-GLY.1 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:F.68, A:F.80, A:Y.88, A:I.118, A:F.139, A:F.139 Hydrogen bonds: A:A.34, A:G.35, A:T.38, A:T.38, A:F.45, A:R.46, A:R.46, A:R.46, A:Q.116, A:H.136, A:T.211, A:T.211, A:T.211, A:S.212, A:S.212, A:N.235, A:K.236, A:C.273 Water bridges: A:S.39, A:S.47, A:S.47, A:Q.116, A:D.274 Salt bridges: A:R.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Deacylation Mechanism by SIRT2 Revealed in the 1'-SH-2'-O-Myristoyl Intermediate Structure. Cell Chem Biol (2017)

Release Date

2016-01-13

Peptides

NAD-dependent protein deacetylase sirtuin-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NAD-dependent protein deacetylase sirtuin-2

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