SMTL ID : 7x3p.1

Crystal structure of human SIRT5 in complex with diazirine inhibitor 9

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

monomer

Ligands

1 x 8VG: 5-[[(5~{S})-6-[[(1~{S})-1-(4-hydroxyphenyl)-2-oxidanylidene-2-(prop-2-ynylamino)ethyl]amino]-6-oxidanylidene-5-[[4-[3-(trifluoromethyl)-1,2-diazirin-3-yl]phenyl]carbonylamino]hexyl]amino]-5-sulfanylidene-pentanoic acid(Non-covalent)

8VG.1: 17 residues within 4Å: Chain A: A.49, Q.50, A.53, Y.69, R.72, I.109, H.125, V.188, W.189, F.190, G.191, E.192, N.193, V.220, V.221, Y.222, P.223 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.109, A:I.109, A:H.125, A:V.188, A:F.190, A:N.193, A:V.221 Hydrogen bonds: A:V.188, A:G.191, A:E.192, A:Y.222, A:Y.222 Water bridges: A:Q.50, A:N.193 Salt bridges: A:R.72 Halogen bonds: A:N.193

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 8 residues within 4Å: Chain A: A.26, G.27, R.38, Q.107, G.216, T.217, S.218, N.242 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:A.26, A:G.27, A:R.38, A:R.38, A:Q.107, A:T.217, A:S.218, A:N.242 Water bridges: A:G.27, A:S.219, A:N.242, A:T.243, A:T.243

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.133, C.136, C.174, C.179 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.133, A:C.136, A:C.174, A:C.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, G.-B. et al., Crystal structure of human SIRT5 in complex with diazirine inhibitor 9. To Be Published

Release Date

2023-09-06

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