SMTL ID : 6l66.1

Sirtuin 2 protein with H3K18 myristoylated peptide and intact NAD molecule

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 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: Y.53, E.65, H.136, V.182, F.183, F.184, G.185, E.186, S.187, L.188, Q.214, V.215, Q.216, P.217 Ligands: 3LX.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:E.65, A:F.184, A:L.188, A:V.215 Hydrogen bonds: A:V.182, A:G.185, A:G.185, A:E.186, A:S.187, A:Q.214, A:Q.214, A:Q.216, A:Q.216

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

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.3: 26 residues within 4Å: Chain A: G.33, A.34, G.35, S.37, T.38, I.42, P.43, D.44, F.45, R.46, Q.116, N.117, I.118, D.119, H.136, G.210, T.211, S.212, V.215, N.235, K.236, E.237, G.271, E.272, C.273 Ligands: 3LX.4 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:A.34 Hydrogen bonds: A:A.34, A:G.35, A:S.37, A:T.38, A:T.38, A:F.45, A:R.46, A:Q.116, A:Q.116, A:I.118, A:D.119, A:D.119, A:H.136, A:G.210, A:T.211, A:S.212, A:S.212, A:L.213, A:N.235, A:K.236, A:K.236, A:E.237, A:C.273 Water bridges: A:S.39, A:D.274 pi-Cation interactions: A:K.236, A:K.236

1 x 3LX: tridecanethial(Non-covalent)

3LX.4: 11 residues within 4Å: Chain A: F.68, L.87, Y.88, I.118, H.136, F.139, I.181, V.182, F.184 Ligands: PRO-ARG-LYS-GLN-LEU-ALA.1, NAD.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.68, A:L.87, A:Y.88, A:I.118, A:F.139, A:F.139, A:I.181

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

2020-11-04

Peptides

NAD-dependent protein deacetylase sirtuin-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NAD-dependent protein deacetylase sirtuin-2