SMTL ID : 6fkz.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-dimer

Ligands

1 x GZB- VAL- LEU- DQK- GLU- TYR- GLY- VAL: 3(S)-(phenylthio)succinyl-CPS1 peptide(Non-covalent)

GZB-VAL-LEU-DQK-GLU-TYR-GLY-VAL.1: 27 residues within 4Å: Chain A: T.44, R.46, A.57, A.61, Y.77, R.80, I.117, H.133, V.195, V.196, W.197, F.198, E.200, T.201, L.202, L.207, Y.230, A.233, M.234 Ligands: GZB-VAL-LEU-EYZ-GLU-TYR-GLY-VAL.2, GZB-VAL-LEU-EYZ-GLU-TYR-GLY-VAL.2, GZB-VAL-LEU-EYZ-GLU-TYR-GLY-VAL.2, GZB-VAL-LEU-EYZ-GLU-TYR-GLY-VAL.2, GZB-VAL-LEU-EYZ-GLU-TYR-GLY-VAL.2, GZB-VAL-LEU-EYZ-GLU-TYR-GLY-VAL.2, GZB-VAL-LEU-EYZ-GLU-TYR-GLY-VAL.2, GZB-VAL-LEU-EYZ-GLU-TYR-GLY-VAL.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:A.57, A:H.133, A:F.198, A:F.198, A:T.201, A:L.202, A:L.207, A:Y.230, A:Y.230 Hydrogen bonds: A:R.46, A:Y.77, A:V.196, A:V.196, A:E.200, A:L.202 Salt bridges: A:R.80 pi-Stacking: A:Y.230

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

GZB-VAL-LEU-EYZ-GLU-TYR-GLY-VAL.2: 27 residues within 4Å: Chain A: T.44, R.46, A.57, A.61, Y.77, R.80, I.117, H.133, V.195, V.196, W.197, F.198, E.200, T.201, L.202, L.207, Y.230, A.233, M.234 Ligands: GZB-VAL-LEU-DQK-GLU-TYR-GLY-VAL.1, GZB-VAL-LEU-DQK-GLU-TYR-GLY-VAL.1, GZB-VAL-LEU-DQK-GLU-TYR-GLY-VAL.1, GZB-VAL-LEU-DQK-GLU-TYR-GLY-VAL.1, GZB-VAL-LEU-DQK-GLU-TYR-GLY-VAL.1, GZB-VAL-LEU-DQK-GLU-TYR-GLY-VAL.1, GZB-VAL-LEU-DQK-GLU-TYR-GLY-VAL.1, GZB-VAL-LEU-DQK-GLU-TYR-GLY-VAL.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.57, A:F.198, A:F.198, A:T.201, A:L.202, A:L.207, A:Y.230, A:Y.230 Hydrogen bonds: A:R.46, A:Y.77, A:V.196, A:E.200, A:L.202 Salt bridges: A:R.80 pi-Stacking: A:Y.230

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: C.141, C.144, C.182, R.184, C.187 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.141, A:C.144, A:C.182, A:C.187 ZN.5: 5 residues within 4Å: Chain B: C.141, C.144, C.182, R.184, C.187 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.141, B:C.144, B:C.182, B:C.187

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: I.155, C.156, L.179, P.180, R.181, E.183 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.152, A:I.155, A:R.181, A:E.183

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.6: 11 residues within 4Å: Chain B: A.57, A.61, Y.77, R.80, H.133, V.196, W.197, F.198, E.200, L.202, Y.230 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.230 Salt bridges: B: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

2018-05-16

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD-dependent protein deacylase sirtuin-5, mitochondrial

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