SMTL ID : 8z58.1

Crystal structure of human N141V-SIRT5 in complex with succinylated Prx1 fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

monomer

Ligands

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

PHE-SER-SLL-GLN.1: 17 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, V.225, V.226, Y.227, P.228 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.199, A:Y.227, A:P.228 Hydrogen bonds: A:Y.74, A:V.193, A:G.196, A:E.197, A:L.199, A:V.225, A:Y.227 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

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 1 residues within 4Å: Chain A: Y.148 Ligand excluded by PLIP

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