SMTL ID : 6ace.1

histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

1 x THR- ILE- MET- PRO- SLL- ASP- ILE- GLN: succinyl peptide H3K122(Non-covalent)

THR-ILE-MET-PRO-SLL-ASP-ILE-GLN.1: 16 residues within 4Å: Chain A: Q.48, Y.67, R.70, I.107, H.123, V.185, V.186, W.187, F.188, G.189, E.190, N.191, V.218, V.219, Y.220, P.221 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Q.48, A:V.186, A:F.188, A:F.188, A:Y.220 Hydrogen bonds: A:Y.67, A:Y.67, A:V.186, A:G.189, A:E.190, A:V.218, A:Y.220, A:Y.220 Water bridges: A:Y.220 Salt bridges: A:R.70

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.131, C.134, C.172, C.177 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.131, A:C.134, A:C.172, A:C.177

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: A.24, V.32, T.34, R.70, N.106, I.107, D.108, L.126 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.27, A:R.70, A:I.107, A:D.108 Water bridges: A:R.70 GOL.4: 4 residues within 4Å: Chain A: E.109, K.113, F.127, Y.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.141, A:Y.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hang, T.R. et al., complex structure of histone lysine desuccinylase Sirt5 with succinyl peptide H3K122. To Be Published

Release Date

2019-07-24

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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