SMTL ID : 4f56.1 (1 other biounit)

The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.137, C.140, C.178, C.183 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.137, A:C.140, A:C.178, A:C.183

1 x CGK: 3-[(2R,3aR,5R,6R,6aR)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-2,6-dihydroxytetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]propanoic acid(Non-covalent)

CGK.2: 28 residues within 4Å: Chain A: G.29, A.30, G.31, A.34, E.35, T.40, F.41, R.42, A.57, Y.73, R.76, Q.111, I.113, H.129, V.191, V.192, F.194, G.220, T.221, S.222, V.225, N.246, T.247, E.248, G.262, P.263, C.264 Chain B: K.6 27 PLIP interactions: 26 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.57, A:V.191 Hydrogen bonds: A:A.30, A:E.35, A:E.35, A:F.41, A:R.42, A:R.42, A:R.42, A:Y.73, A:Y.73, A:Q.111, A:T.221, A:T.221, A:T.221, A:S.222, A:S.222, A:N.246, A:T.247, A:T.247, A:T.247, A:C.264 Water bridges: A:E.35, A:E.248 Salt bridges: A:R.42, A:R.76, B:K.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, Y. et al., The Bicyclic Intermediate Structure Provides Insights into the Desuccinylation Mechanism of Human Sirtuin 5 (SIRT5). J.Biol.Chem. (2012)

Release Date

2012-06-20

Peptides

NAD-dependent lysine demalonylase and desuccinylase sirtuin-5, mitochondrial: A
peptide from Histone H3.1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

NAD-dependent lysine demalonylase and desuccinylase sirtuin-5, mitochondrial

peptide from Histone H3.1

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