SMTL ID : 5oj7.1

Sirtuin 4 orthologue from Xenopus Tropicalis in complex with ADP-ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

monomer

Ligands

1 x AR6: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE(Non-covalent)

AR6.1: 25 residues within 4Å: Chain A: V.3, P.4, G.32, A.33, G.34, T.37, E.38, D.43, Y.44, R.45, S.46, Q.113, H.131, G.230, S.231, S.232, L.233, V.235, N.256, I.257, G.258, A.272, R.273, C.274 Ligands: GOL.7 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:A.33, A:E.38, A:E.38, A:Y.44, A:R.45, A:R.45, A:Q.113, A:H.131, A:S.232, A:L.233, A:N.256, A:I.257, A:G.258, A:P.259, A:C.274 Water bridges: A:E.38, A:E.38, A:Y.44, A:R.45, A:T.202, A:Q.234 Salt bridges: A:R.45, A:R.45

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.139, C.142, C.190, C.193 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.139, A:C.142, A:C.190, A:C.193

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

EDO.3: 5 residues within 4Å: Chain A: H.131, G.132, Q.200, V.201, T.202 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.200 Water bridges: A:R.136, A:Q.200, A:T.202, A:D.206 EDO.4: 4 residues within 4Å: Chain A: R.74, Y.75, R.78, D.174 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.174 Water bridges: A:I.60, A:Y.75, A:D.174 EDO.5: 1 residues within 4Å: Chain A: F.212 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.129 EDO.6: 6 residues within 4Å: Chain A: W.109, L.127, S.128, F.212, S.215, Q.219 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.128, A:Q.219 Water bridges: A:S.215

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: H.131, T.202, F.203, F.204, D.206, V.235, S.237 Ligands: AR6.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.202, A:D.206, A:S.237 Water bridges: A:V.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pannek, M. et al., Crystal structures of the mitochondrial deacylase Sirtuin 4 reveal isoform-specific acyl recognition and regulation features. Nat Commun (2017)

Release Date

2017-11-29

Peptides

NAD-dependent protein deacylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NAD-dependent protein deacylase

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