SMTL ID : 6ljk.1

Crystal structure of human Sirt5 in complex with an internally quenched fluorescent substrate GluIQF

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

monomer

Ligands

1 x BE2- SER- ALA- ILE- LYS- SER- NIY- GLY- SET: BE2-SER-ALA-ILE-LYS-SER-NIY-GLY-SET(Non-covalent)

BE2-SER-ALA-ILE-LYS-SER-NIY-GLY-SET.1: 18 residues within 4Å: Chain A: R.41, Q.53, H.128, V.191, W.192, F.193, G.194, E.195, N.196, L.197, L.202, V.223, V.224, Y.225, P.226, M.229, Q.233 Ligands: GUA.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Q.53, A:L.197, A:L.202, A:V.224, A:V.224 Hydrogen bonds: A:V.191, A:G.194, A:E.195, A:L.197, A:V.223, A:Y.225, A:Y.225 Water bridges: A:Q.53, A:N.196

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 8 residues within 4Å: Chain A: C.136, S.138, C.139, V.141, 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 NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: G.28, A.29, Q.110, T.220, S.221 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.29, A:T.220, A:S.221, A:S.221 Water bridges: A:G.30, A:R.41, A:S.222

1 x GUA: GLUTARIC ACID(Non-covalent)

GUA.4: 15 residues within 4Å: Chain A: R.41, A.52, A.56, F.71, Y.72, R.75, Q.110, I.112, H.128, V.190, V.191, W.192, F.193, V.224 Ligands: BE2-SER-ALA-ILE-LYS-SER-NIY-GLY-SET.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.112, A:H.128 Hydrogen bonds: A:R.41, A:R.41, A:Y.72 Water bridges: A:R.75 Salt bridges: A:R.41, A:R.75

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

2020-12-23

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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