SMTL ID : 6xv6.1 (5 other biounits)

Human Sirt6 3-318 in complex with ADP-ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 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: Y.3, L.7, G.50, A.51, G.52, T.55, D.61, F.62, R.63, Q.111, H.131, G.212, T.213, S.214, I.217, N.238, L.239, Q.240, G.254, Y.255, V.256 Ligands: GOL.5 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:Y.3, A:A.51, A:T.55, A:T.55, A:F.62, A:R.63, A:R.63, A:Q.111, A:S.214, A:N.238, A:L.239, A:Q.240, A:Q.240, A:V.256 Water bridges: A:E.20, A:T.55, A:D.257 Salt bridges: A:R.63, A:R.63

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.139, C.142, C.164, C.175 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.139, A:C.142, A:C.164, A:C.175

1 x NCA: NICOTINAMIDE(Non-covalent)

NCA.3: 9 residues within 4Å: Chain A: Y.3, A.51, I.59, P.60, F.62, F.84, N.112, V.113, D.114 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.3, A:I.59, A:F.84, A:V.113 Hydrogen bonds: A:V.113, A:D.114, A:D.114 pi-Stacking: A:F.62

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: W.40, H.266, G.268, P.290, P.291, P.293 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.40 GOL.5: 8 residues within 4Å: Chain A: Y.3, L.7, L.184, D.185, W.186, L.190, I.217 Ligands: AR6.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.184

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

SO4.6: 5 residues within 4Å: Chain A: D.23, E.27, K.31, R.251, H.253 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.27 Water bridges: A:R.251 Salt bridges: A:K.31, A:H.253 SO4.7: 5 residues within 4Å: Chain A: V.151, V.152, G.153, T.160, R.162 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.153, A:T.160 Salt bridges: A:R.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

You, W. et al., Binding site for activator MDL-801 on SIRT6. Nat.Chem.Biol. (2021)

Release Date

2020-10-28

Peptides

NAD-dependent protein deacetylase sirtuin-6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NAD-dependent protein deacetylase sirtuin-6

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