SMTL ID : 6zu4.1

Human Sirt6 13-308 in complex with ADP-ribose and the activator fluvastatin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

homo-dimer

Ligands

2 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 Chain B: D.77 18 PLIP interactions: 18 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:Q.107, A:H.127, A:S.210, A:L.211, A:N.234, A:L.235, A:Q.236, A:Q.236, A:V.252 Salt bridges: A:R.59, A:R.59 AR6.8: 22 residues within 4Å: Chain A: D.77 Chain B: 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 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:A.47, B:T.51, B:F.58, B:R.59, B:R.59, B:T.209, B:S.210, B:N.234, B:L.235, B:Q.236, B:Q.236, B:V.252 Salt bridges: B:R.59, B:R.59

2 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 ZN.9: 4 residues within 4Å: Chain B: C.135, C.138, C.160, C.171 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.135, B:C.138, B:C.160, B:C.171

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: F.18, Y.251 Chain B: T.78, T.79 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.251 GOL.11: 5 residues within 4Å: Chain A: F.76, T.78, T.79 Chain B: F.18, Y.251 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.251, A:T.78

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

SO4.4: 1 residues within 4Å: Chain A: K.290 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.290 SO4.5: 4 residues within 4Å: Chain A: E.23, K.27, R.247, H.249 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.23 Salt bridges: A:K.27, A:R.247, A:H.249 SO4.6: 3 residues within 4Å: Chain A: R.199, R.225, R.226 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.225, A:R.226 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 SO4.12: 5 residues within 4Å: Chain A: H.62, D.77 Chain B: H.62, K.75, D.77 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.62, A:H.62 SO4.13: 3 residues within 4Å: Chain B: K.27, R.247, H.249 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.27, B:R.247, B:H.249 SO4.14: 1 residues within 4Å: Chain B: K.290 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.290 SO4.15: 3 residues within 4Å: Chain B: R.214, P.215, N.218 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.218 Salt bridges: B:R.214 SO4.16: 6 residues within 4Å: Chain A: R.84, A.269, W.270 Chain B: R.84, A.269, W.270 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:W.270, A:W.270 Salt bridges: B:R.84, A:R.84

1 x 115: (3R,5S,6E)-7-[3-(4-fluorophenyl)-1-(propan-2-yl)-1H-indol-2-yl]-3,5-dihydroxyhept-6-enoic acid(Non-covalent)

115.10: 14 residues within 4Å: Chain B: K.9, I.55, P.56, F.58, V.64, W.65, E.68, P.74, F.76, F.80, V.109, M.151, I.179, W.182 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.55, B:V.64, B:P.74, B:F.76, B:F.76, B:I.179 Hydrogen bonds: B:E.68 Salt bridges: B:K.9 pi-Stacking: B:F.58, B:F.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

You, W. et al., Structural Basis for Activation of Human Sirtuin 6 by Fluvastatin. Acs Med.Chem.Lett. (2020)

Release Date

2020-11-18

Peptides

NAD-dependent protein deacetylase sirtuin-6: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD-dependent protein deacetylase sirtuin-6

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