SMTL ID : 6ljm.1

Crystal structure of human Sirt5 in complex with the fluorogenic tetrapeptide substrate P13

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

1 x ACE- SER- LEU- GLY- SLL: ACE-SER-LEU-GLY-SLL(Non-covalent)

ACE-SER-LEU-GLY-SLL.1: 19 residues within 4Å: Chain A: R.41, Q.53, D.54, A.56, T.57, P.58, F.71, Y.72, R.75, I.112, H.128, V.190, V.191, W.192, F.193, G.194, L.197, Y.225 Ligands: MCM.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.191, A:Y.225 Hydrogen bonds: A:R.41, A:R.41, A:Q.53, A:Y.72, A:Y.72, A:H.128, A:V.191 Water bridges: A:T.57, A:T.57, A:T.57, A:Q.110 Salt bridges: A:R.75

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: C.136, S.138, C.139, C.177, E.179, C.182, G.184 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.136, A:C.139, A:C.177, A:C.182

1 x MCM: 7-AMINO-4-METHYL-CHROMEN-2-ONE(Non-covalent)

MCM.3: 7 residues within 4Å: Chain A: E.195, N.196, L.197, L.202, Y.225, M.229 Ligands: ACE-SER-LEU-GLY-SLL.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.197, A:L.202, A:Y.225

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, L.L. et al., Sensitive fluorogenic substrates for sirtuin deacylase inhibitor discovery. Eur.J.Med.Chem. (2020)

Release Date

2020-10-28

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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