SMTL ID : 3d4b.1

Crystal structure of Sir2Tm in complex with Acetyl p53 peptide and DADMe-NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x THR- SER- ARG- HIS- LYS- ALY- LEU- MET- ALA: Acetyl P53 peptide(Non-covalent)

THR-SER-ARG-HIS-LYS-ALY-LEU-MET-ALA.1: 17 residues within 4Å: Chain A: F.48, H.116, V.160, F.161, F.162, G.163, E.164, N.165, L.166, P.167, Q.168, L.171, V.192, V.193, Y.194, P.195 Ligands: DZD.3 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:F.48, A:V.160, A:F.162, A:F.162, A:L.166, A:L.171, A:V.193, A:Y.194, A:P.195 Hydrogen bonds: A:V.160, A:G.163, A:E.164, A:N.165, A:N.165, A:N.165, A:L.166, A:L.166, A:L.166, A:V.192, A:Y.194, A:Y.194 Water bridges: A:Q.168, A:Q.168

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.124, C.127, C.148, C.151 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.124, A:C.127, A:C.148, A:C.151

1 x DZD: 5'-O-[(R)-{[(R)-{[(3R,4R)-1-(3-carbamoylbenzyl)-4-hydroxypyrrolidin-3-yl]methoxy}(hydroxy)phosphoryl]methyl}(hydroxy)phosphoryl]adenosine(Non-covalent)

DZD.3: 28 residues within 4Å: Chain A: G.21, A.22, G.23, S.25, T.26, P.27, I.30, P.31, D.32, F.33, Q.98, N.99, I.100, D.101, H.116, F.162, G.188, S.189, S.190, L.191, V.193, N.214, L.215, G.216, M.230, D.231, V.232 Ligands: THR-SER-ARG-HIS-LYS-ALY-LEU-MET-ALA.1 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:A.22, A:I.30, A:F.33, A:V.193 Hydrogen bonds: A:A.22, A:T.26, A:T.26, A:F.33, A:Q.98, A:I.100, A:D.101, A:D.101, A:S.189, A:S.190, A:S.190, A:L.191, A:N.214, A:L.215, A:G.216, A:D.231, A:V.232 pi-Stacking: A:F.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hawse, W.F. et al., Structural insights into intermediate steps in the Sir2 deacetylation reaction. Structure (2008)

Release Date

2008-09-30

Peptides

NAD-dependent deacetylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NAD-dependent deacetylase

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