SMTL ID : 6l71.1

Sirtuin 2 demyristoylation native intermediate I & II mixture

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

monomer

Ligands

1 x PRO- ARG- LYS- GLN- LEU- ALA: PRO-ARG-LYS-GLN-LEU-ALA(Non-covalent)

PRO-ARG-LYS-GLN-LEU-ALA.1: 15 residues within 4Å: Chain A: R.46, E.65, H.136, V.182, F.183, F.184, G.185, E.186, L.188, Q.214, V.215, Q.216, P.217 Ligands: YOY.3, YDD.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:E.65, A:V.182, A:F.184, A:F.184, A:L.188, A:V.215 Hydrogen bonds: A:G.185, A:E.186, A:Q.216, A:Q.216

1 x NCA: NICOTINAMIDE(Non-covalent)

NCA.2: 11 residues within 4Å: Chain A: A.34, S.37, I.42, P.43, D.44, F.45, N.117, I.118, D.119 Ligands: YOY.3, YDD.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.34 Hydrogen bonds: A:I.118, A:D.119, A:D.119 pi-Stacking: A:F.45

1 x YOY: [[(2S,3aS,5S,6R,6aS)-2-dodecyl-6-oxidanyl-3a,5,6,6a-tetrahydrofuro[2,3-d][1,3]dioxol-5-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

YOY.3: 30 residues within 4Å: Chain A: G.33, A.34, G.35, T.38, D.44, F.45, R.46, F.68, L.87, P.89, Q.116, I.118, H.136, F.139, I.181, 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-ARG-LYS-GLN-LEU-ALA.1, NCA.2, YDD.4 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:F.68, A:L.87, A:I.118, A:I.118, A:F.139, A:F.139, A:I.181 Hydrogen bonds: A:A.34, A:G.35, A:D.44, A:F.45, A:R.46, A:R.46, A:Q.116, A:Q.116, A:H.136, A:T.211, A:T.211, A:S.212, A:S.212, A:N.235, A:K.236, A:E.237, A:E.237, A:E.272, A:C.273 Water bridges: A:S.39, A:S.47, A:E.272, A:D.274 Salt bridges: A:R.46, A:H.136, A:H.136

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

YDD.4: 38 residues within 4Å: Chain A: G.33, A.34, G.35, T.38, D.44, F.45, R.46, S.47, F.68, F.80, A.84, L.87, Y.88, P.89, F.92, Q.116, I.118, D.119, H.136, F.139, I.181, V.182, F.183, F.184, G.210, T.211, S.212, L.213, V.215, N.235, K.236, E.237, G.271, E.272, C.273 Ligands: PRO-ARG-LYS-GLN-LEU-ALA.1, NCA.2, YOY.3 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:F.45, A:F.68, A:F.68, A:Y.88, A:F.92, A:I.118, A:F.139, A:F.139, A:I.181 Hydrogen bonds: A:A.34, A:G.35, A:F.45, A:R.46, A:R.46, A:Q.116, A:Q.116, A:H.136, A:H.136, A:T.211, A:T.211, A:S.212, A:L.213, A:N.235, A:K.236, A:E.237, A:E.272, A:C.273 Water bridges: A:T.38, A:S.47, A:Q.214, A:E.272, A:D.274 Salt bridges: A:R.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, L.F., Sirtuin 2 protein with H3K18 myristoylated peptide. To Be Published

Release Date

2021-03-31

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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