SMTL ID : 4fvt.1

Human SIRT3 bound to Ac-ACS peptide and Carba-NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

monomer

Ligands

1 x SER- GLY- ALY- VAL- NLE: Acetylated ACS2 peptide(Non-covalent)

SER-GLY-ALY-VAL-NLE.1: 16 residues within 4Å: Chain A: E.56, F.59, H.127, I.170, V.171, F.172, F.173, G.174, E.175, P.176, L.177, E.202, V.203, E.204, P.205 Ligands: CNA.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.59, A:H.127, A:I.170, A:F.173, A:F.173, A:L.177, A:V.203 Hydrogen bonds: A:H.127, A:V.171, A:G.174, A:E.175, A:E.204, A:E.204

1 x CNA: CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

CNA.2: 24 residues within 4Å: Chain A: G.24, A.25, G.26, T.29, I.33, P.34, D.35, F.36, F.59, Q.107, N.108, I.109, D.110, H.127, G.198, T.199, S.200, V.203, N.223, R.224, G.243, D.244, V.245 Ligands: SER-GLY-ALY-VAL-NLE.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.203 Hydrogen bonds: A:A.25, A:G.26, A:T.29, A:T.29, A:Q.107, A:I.109, A:D.110, A:D.110, A:S.200, A:S.200, A:L.201, A:N.223, A:R.224, A:R.224, A:V.245 pi-Cation interactions: A:R.224

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

SO4.3: 2 residues within 4Å: Chain A: V.156, R.158 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.156 Salt bridges: A:R.158 SO4.4: 2 residues within 4Å: Chain A: P.178, Q.179 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.179 SO4.5: 4 residues within 4Å: Chain A: R.93, R.268, E.269, K.272 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.269 Salt bridges: A:R.93, A:K.272

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain A: C.135, C.138, C.159, C.162 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.135, A:C.138, A:C.159, A:C.162

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: G.99, L.101, K.122 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Szczepankiewicz, B.G. et al., Synthesis of Carba-NAD and the Structures of Its Ternary Complexes with SIRT3 and SIRT5. J.Org.Chem. (2012)

Release Date

2012-08-15

Peptides

NAD-dependent protein deacetylase sirtuin-3, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NAD-dependent protein deacetylase sirtuin-3, mitochondrial

Related Entries With Identical Sequence