SMTL ID : 8z54.1

Crystal structure of human SIRT5 in complex with succinylated Prx1 fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x PHE- SER- SLL- GLN: Peroxiredoxin-1 fragment(Non-covalent)

PHE-SER-SLL-GLN.1: 18 residues within 4Å: Chain A: A.58, Y.74, R.77, I.114, H.130, V.192, V.193, W.194, F.195, G.196, E.197, N.198, L.199, L.204, V.225, V.226, Y.227, P.228 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.58, A:V.192, A:L.204, A:Y.227 Hydrogen bonds: A:Y.74, A:V.193, A:G.196, A:E.197, A:L.199, A:Y.227, A:Y.227 Water bridges: A:H.130 Salt bridges: A:R.77

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.138, C.141, C.179, C.184 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.138, A:C.141, A:C.179, A:C.184

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 4 residues within 4Å: Chain A: A.94, E.95, T.98, A.121 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.98 DMS.4: 5 residues within 4Å: Chain A: D.56, L.57, L.61, H.65, R.69 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yokoyama, T. et al., SIRT5 mutants reveal the role of conserved asparagine and glutamine residues in the NAD + -binding pocket. Febs Lett. (2024)

Release Date

2024-10-09

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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