SMTL ID : 5mfp.2 (1 other biounit)

Human Sirt6 in complex with activator UBCS58

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 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: 22 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 Ligands: PGE.7 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:A.47, A:G.48, A:T.51, A:T.51, A:F.58, A:R.59, A:R.59, A:H.127, A:S.210, A:L.211, A:N.234, A:L.235, A:Q.236, A:Q.236, A:V.252 Water bridges: A:A.52, A:Q.107 Salt bridges: 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

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

SO4.3: 2 residues within 4Å: Chain A: H.62, K.75 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.62, A:K.75, A:D.77 Salt bridges: A:H.62 SO4.4: 3 residues within 4Å: Chain A: K.27, R.247, H.249 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.247 Salt bridges: A:K.27, A:R.247, A:H.249 SO4.5: 1 residues within 4Å: Chain A: K.290 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.290 SO4.6: 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

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 9 residues within 4Å: Chain A: H.127, L.180, D.181, W.182, D.184, L.186, I.213, R.214 Ligands: AR6.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.182

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

EDO.8: 4 residues within 4Å: Chain A: R.97, L.280, P.281, L.283 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.97 Water bridges: A:R.97 EDO.9: 1 residues within 4Å: Chain A: R.97 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.97, A:R.97

1 x 7M5: 4-pyridin-3-ylpyrrolo[1,2-a]quinoxaline(Non-covalent)

7M5.10: 9 residues within 4Å: Chain A: I.55, P.56, F.58, V.64, F.76, F.80, V.109, M.151, I.179 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.80, A:I.179 pi-Stacking: A:F.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

You, W. et al., Structural Basis of Sirtuin 6 Activation by Synthetic Small Molecules. Angew. Chem. Int. Ed. Engl. (2017)

Release Date

2016-12-28

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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