SMTL ID : 6qch.2 (1 other biounit)

Human Sirt6 in complex with ADP-ribose and the activator cyanidin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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: 21 residues within 4Å: Chain A: G.46, A.47, G.48, T.51, D.57, F.58, R.59, W.65, Q.107, H.127, W.182, G.208, T.209, S.210, I.213, N.234, L.235, Q.236, G.250, Y.251, V.252 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:A.47, A:G.48, A:T.51, A:F.58, A:R.59, A:G.60, A:T.209, A:S.210, A:N.234, A:L.235, A:Q.236, A:Q.236, A:V.252 Water bridges: A:T.51, A:L.211, A:L.211, A:Q.212, A:D.253 Salt bridges: A:R.59, A:R.59, A:R.59

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.135, C.138, C.160, C.171 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.135, A:C.138, A:C.160, A:C.171

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

EDO.3: 5 residues within 4Å: Chain A: R.97, L.280, P.281, L.283 Ligands: SO4.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.97

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

SO4.4: 2 residues within 4Å: Chain A: H.62, K.75 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.54 Salt bridges: A:H.62 SO4.5: 4 residues within 4Å: Chain A: E.23, K.27, R.247, H.249 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.27, A:R.247, A:H.249 SO4.6: 1 residues within 4Å: Chain A: K.290 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.290 SO4.7: 3 residues within 4Å: Chain A: R.214, P.215, N.218 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.218 Salt bridges: A:R.214 SO4.8: 4 residues within 4Å: Chain A: R.84, P.268, A.269, W.270 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.268, A:W.270 Salt bridges: A:R.84 SO4.9: 2 residues within 4Å: Chain A: P.281 Ligands: EDO.3 No protein-ligand interaction detected (PLIP)

1 x HWB: cyanidin(Non-covalent)

HWB.10: 12 residues within 4Å: Chain A: A.47, I.55, P.56, F.58, V.64, P.74, F.76, F.80, V.109, D.110, M.130, M.151 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.64, A:F.76, A:F.76, A:F.80 Hydrogen bonds: A:P.56 pi-Stacking: A:F.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

You, W. et al., Structural basis for the activation and inhibition of Sirtuin 6 by quercetin and its derivatives. Sci Rep (2019)

Release Date

2019-12-25

Peptides

NAD-dependent protein deacetylase sirtuin-6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

NAD-dependent protein deacetylase sirtuin-6

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