SMTL ID : 7cl0.1

Crystal structure of human SIRT6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

monomer

Ligands

1 x THR- ALA- ARG- LYS- SER- THR- GLY: THR-ALA-ARG-LYS-SER-THR-GLY(Non-covalent)

THR-ALA-ARG-LYS-SER-THR-GLY.1: 19 residues within 4Å: Chain A: D.14, H.133, L.186, D.187, W.188, E.189, D.190, S.191, L.192, L.197, Q.218, I.219, R.220, P.221 Ligands: AR6.2, SO4.6, EDO.17, G4U.20, PEG.21 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.192, A:L.197, A:I.219, A:I.219 Hydrogen bonds: A:D.14, A:D.14, A:E.189, A:D.190, A:L.192, A:R.220, A:R.220, A:R.220, A:K.245 Water bridges: A:H.133

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)

AR6.2: 23 residues within 4Å: Chain A: G.52, A.53, G.54, T.57, D.63, F.64, R.65, W.71, Q.113, H.133, G.214, T.215, S.216, I.219, N.240, L.241, Q.242, G.256, Y.257, V.258 Ligands: THR-ALA-ARG-LYS-SER-THR-GLY.1, SO4.8, G4U.20 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:A.53, A:G.54, A:T.57, A:T.57, A:F.64, A:R.65, A:G.66, A:Q.113, A:T.215, A:T.215, A:S.216, A:L.217, A:N.240, A:L.241, A:Q.242, A:Q.242, A:V.258 Water bridges: A:E.22, A:T.57, A:R.65 Salt bridges: A:R.65, A:R.65, A:R.65

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.141, C.144, C.166, C.177 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.141, A:C.144, A:C.166, A:C.177

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

SO4.4: 4 residues within 4Å: Chain A: D.25, K.33, R.253, H.255 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.253 Salt bridges: A:K.33, A:R.253, A:H.255 SO4.5: 6 residues within 4Å: Chain A: R.220, P.221, N.224 Ligands: EDO.16, EDO.17, PEG.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.224 SO4.6: 2 residues within 4Å: Chain A: E.189 Ligands: THR-ALA-ARG-LYS-SER-THR-GLY.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.189 Water bridges: A:E.189 SO4.7: 4 residues within 4Å: Chain A: R.126, T.146, Q.147, E.283 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.126, A:Q.147, A:E.283 Water bridges: A:Q.147, A:Q.147, A:V.149 SO4.8: 4 residues within 4Å: Chain A: E.22, T.57, Y.257 Ligands: AR6.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.57 Water bridges: A:E.22, A:E.22, A:E.22, A:D.63 SO4.9: 2 residues within 4Å: Chain A: K.267, H.268 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.267, A:H.268 SO4.10: 3 residues within 4Å: Chain A: G.158, L.159, K.160 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.159 Water bridges: A:A.161 SO4.11: 9 residues within 4Å: Chain A: I.238, N.240, Q.242, P.243, T.244, D.247, R.253, I.254, H.255 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.238, A:N.240, A:Q.242, A:T.244 Salt bridges: A:H.255

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

EDO.12: 4 residues within 4Å: Chain A: S.10, K.15, W.71, E.74 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.15, A:E.74 EDO.13: 3 residues within 4Å: Chain A: L.159, S.191, P.193 No protein-ligand interaction detected (PLIP) EDO.14: 1 residues within 4Å: Chain A: R.182 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.182, A:R.182 EDO.15: 3 residues within 4Å: Chain A: A.161, T.162, G.163 No protein-ligand interaction detected (PLIP) EDO.16: 3 residues within 4Å: Chain A: R.220, N.224 Ligands: SO4.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.220, A:N.224 Water bridges: A:K.245 EDO.17: 5 residues within 4Å: Chain A: D.201, P.221, L.225 Ligands: THR-ALA-ARG-LYS-SER-THR-GLY.1, SO4.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.201 EDO.18: 3 residues within 4Å: Chain A: T.263, E.272, I.273 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.273, A:I.273 EDO.19: 7 residues within 4Å: Chain A: F.109, R.126, D.127, L.129, A.130, D.196, L.199 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.129 Water bridges: A:R.195

1 x G4U: tetradecanethial(Non-covalent)

G4U.20: 12 residues within 4Å: Chain A: L.9, I.61, P.62, F.64, V.70, F.82, F.86, M.157, L.186, W.188 Ligands: THR-ALA-ARG-LYS-SER-THR-GLY.1, AR6.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.9, A:I.61, A:F.64, A:F.64, A:V.70, A:F.82, A:F.86, A:F.86

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.21: 6 residues within 4Å: Chain A: R.220 Ligands: THR-ALA-ARG-LYS-SER-THR-GLY.1, THR-ALA-ARG-LYS-SER-THR-GLY.1, THR-ALA-ARG-LYS-SER-THR-GLY.1, THR-ALA-ARG-LYS-SER-THR-GLY.1, SO4.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, Z. et al., Reply to: Binding site for MDL-801 on SIRT6. Nat.Chem.Biol. (2021)

Release Date

2021-02-24

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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