SMTL ID : 5xhs.1

Crystal structure of SIRT5 complexed with a fluorogenic small-molecule substrate SuBKA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

monomer

Ligands

1 x PHQ: benzyl chlorocarbonate(Non-covalent)

PHQ.1: 3 residues within 4Å: Chain A: F.209, G.210 Ligands: SLL.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.210

1 x SLL: (2S)-2-azanyl-6-[(4-hydroxy-4-oxo-butanoyl)amino]hexanoic acid(Non-covalent)

SLL.2: 17 residues within 4Å: Chain A: R.57, A.68, A.72, Y.88, R.91, I.128, H.144, V.206, V.207, W.208, F.209, G.210, E.211, L.213, Y.241 Ligands: PHQ.1, MCM.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.72 Hydrogen bonds: A:Y.88, A:Y.88, A:H.144, A:V.207 Water bridges: A:R.57 Salt bridges: A:R.91

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

MCM.3: 8 residues within 4Å: Chain A: E.211, N.212, L.213, L.218, Y.241, M.245, F.246 Ligands: SLL.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.213, A:L.213, A:L.218, A:Y.241 Hydrogen bonds: A:E.211

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 7 residues within 4Å: Chain A: C.152, S.154, C.155, C.193, E.195, C.198, G.200 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.152, A:C.155, A:C.193, A:C.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H.L. et al., Interactions between sirtuins and fluorogenic small-molecule substrates offer insights into inhibitor design. Rsc Adv (2017)

Release Date

2018-05-02

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