SMTL ID : 6fky.1 (1 other biounit)

Crystal structure of zebrafish Sirtuin 5 in complex with 3-(benzylthio)succinyl-CPS1 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.98 Å

Oligo State

monomer

Ligands

2 x GZB- VAL- LEU- LYS- GLU- TYR- GLY- VAL: 3(R)-(phenylthio)succinyl-CPS1 peptide(Non-covalent)

GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.1: 22 residues within 4Å: Chain A: R.46, H.133, V.196, W.197, F.198, E.200, T.201, L.202, L.207, Y.230, A.233, M.234 Ligands: GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.2, GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.2, GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.2, GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.2, GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.2, GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.2, GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.2, GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.2, E9N.4, DZK.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.196, A:F.198, A:L.207, A:Y.230, A:Y.230 Hydrogen bonds: A:E.200, A:L.202, A:Y.230, A:A.233 Salt bridges: A:R.46 pi-Stacking: A:Y.230 GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.2: 22 residues within 4Å: Chain A: R.46, H.133, V.196, W.197, F.198, E.200, T.201, L.202, L.207, Y.230, A.233, M.234 Ligands: GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.1, GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.1, GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.1, GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.1, GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.1, GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.1, GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.1, GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.1, E9N.4, DZK.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.196, A:F.198, A:L.207, A:Y.230, A:Y.230 Hydrogen bonds: A:R.46, A:E.200, A:L.202, A:Y.230, A:A.233 pi-Stacking: A:Y.230

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.141, C.144, C.182, C.187 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.141, A:C.144, A:C.182, A:C.187

1 x E9N: (2~{R})-2-(phenylmethylsulfanyl)butanedioic acid(Non-covalent)

E9N.4: 16 residues within 4Å: Chain A: A.34, T.44, R.46, A.61, Y.77, R.80, Q.115, N.116, I.117, H.133, V.195, V.196, W.197 Ligands: GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.1, GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.2, DZK.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.34, A:T.44, A:I.117 Hydrogen bonds: A:Y.77, A:V.196 Salt bridges: A:R.80

1 x DZK: (2~{S})-2-(phenylmethylsulfanyl)butanedioic acid(Non-covalent)

DZK.5: 15 residues within 4Å: Chain A: A.34, T.44, R.46, A.57, A.61, Y.77, R.80, N.116, I.117, H.133, V.196, F.198 Ligands: GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.1, GZB-VAL-LEU-LYS-GLU-TYR-GLY-VAL.2, E9N.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.34, A:T.44, A:I.117, A:F.198 Hydrogen bonds: A:R.46, A:R.46, A:Y.77 Salt bridges: A:R.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kalbas, D. et al., Potent and Selective Inhibitors of Human Sirtuin 5. J. Med. Chem. (2018)

Release Date

2018-03-21

Peptides

NAD-dependent protein deacylase sirtuin-5, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NAD-dependent protein deacylase sirtuin-5, mitochondrial

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