SMTL ID : 8z55.1

Crystal structure of human SIRT5 in complex with succPrx1 and ADP ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

monomer

Ligands

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

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 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.192, A:L.199, A:Y.227 Hydrogen bonds: A:Y.74, A:H.130, A:V.193, A:G.196, A:E.197, A:N.198, A:Y.227, A:Y.227 Salt bridges: A:R.77

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 16 residues within 4Å: Chain A: G.30, A.31, G.32, E.36, R.43, Q.112, G.221, T.222, S.223, V.226, N.247, T.248, E.249, G.263, P.264, C.265 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:A.31, A:G.32, A:E.36, A:Q.112, A:T.222, A:S.223, A:S.223, A:N.247, A:T.248, A:T.248, A:E.249, A:E.249, A:C.265

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 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

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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