SMTL ID : 6qcj.1

Human Sirt6 in complex with ADP-ribose and the inhibitor catechin gallate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 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: 23 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 Ligands: EDO.3 22 PLIP interactions: 22 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:G.60, A:W.65, A:H.127, A:S.210, A:N.234, A:L.235, A:Q.236, A:Q.236, A:V.252 Water bridges: A:Q.107, A:L.211, A:L.211, A:D.253 Salt bridges: A:R.59, A:R.59, A:R.59 AR6.8: 21 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, G.208, T.209, S.210, I.213, N.234, L.235, Q.236, G.250, Y.251, V.252 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:A.47, B:T.51, B:T.51, B:F.58, B:R.59, B:G.60, B:T.209, B:T.209, B:S.210, B:L.211, B:N.234, B:L.235, B:Q.236, B:Q.236, B:V.252 Water bridges: B:R.59, B:Q.212 Salt bridges: B:R.59, 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

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

EDO.3: 5 residues within 4Å: Chain A: H.127, L.180, D.181, W.182 Ligands: AR6.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.180

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

SO4.4: 3 residues within 4Å: Chain A: 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 SO4.5: 3 residues within 4Å: Chain A: R.199, R.225, R.226 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.199, A:R.225, A:R.226 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 SO4.10: 4 residues within 4Å: Chain A: H.62, D.77 Chain B: H.62, K.75 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:H.62, B:H.62 Water bridges: B:D.77, B:D.77 SO4.11: 3 residues within 4Å: Chain B: K.27, R.247, H.249 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.249 Salt bridges: B:K.27, B:R.247 SO4.12: 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 SO4.13: 6 residues within 4Å: Chain A: R.84, A.269, W.270 Chain B: R.84, A.269, W.270 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:W.270, A:W.270, A:W.270 Water bridges: B:R.84, B:R.84 Salt bridges: B:R.84, A:R.84

2 x XEG: (2R,3S)-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate(Non-covalent)

XEG.7: 17 residues within 4Å: Chain A: A.47, I.55, P.56, F.58, V.64, W.65, F.76, F.80, V.109, D.110, M.130, V.147, V.148, G.149, T.150, M.151, I.179 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.58, A:V.64, A:V.64, A:F.76, A:F.80, A:V.109, A:M.130, A:I.179 Hydrogen bonds: A:P.56, A:D.110, A:D.110, A:G.149, A:T.150 Water bridges: A:N.129, A:I.179 XEG.14: 13 residues within 4Å: Chain B: A.47, I.55, P.56, F.58, W.65, F.76, F.80, V.109, D.110, M.130, G.149, T.150, M.151 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.58, B:F.76, B:F.80, B:V.109 Hydrogen bonds: B:P.56, B:D.110, B:M.130, B:G.149

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD-dependent protein deacetylase sirtuin-6

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