SMTL ID : 9cbt.1 (1 other biounit)

Crystal structure of human sirtuin 3 fragment (residues 118-399) bound to intermediates from reaction with NAD and inhibitor NH6-10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.139, C.142, C.163, C.166 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.139, A:C.142, A:C.163, A:C.166

1 x 5IA: 2-{[(2S)-6-[(Z)-(1-{[(2R,3R,4R,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-4-hydroxy-2-sulfanyloxolan-3-yl]oxy}tetradecylidene)amino]-2-{[(benzyloxy)carbonyl]amino}hexanoyl]amino}-N,N,N-triethylethan-1-aminium (non-preferred name)(Non-covalent)

5IA.2: 37 residues within 4Å: Chain A: G.28, A.29, G.30, T.33, I.37, D.39, F.40, R.41, S.42, Y.48, F.63, L.82, Y.87, Q.111, I.113, D.114, H.131, I.174, V.175, F.176, F.177, G.178, E.179, P.180, L.181, G.202, T.203, S.204, V.207, E.208, P.209, N.227, R.228, D.229, G.247, D.248, V.249 43 PLIP interactions: 43 interactions with chain A Hydrophobic interactions: A:I.37, A:F.40, A:F.63, A:F.63, A:L.82, A:L.82, A:Y.87, A:I.113, A:D.114, A:I.174, A:V.175, A:F.177, A:P.180, A:L.181, A:V.207 Hydrogen bonds: A:A.29, A:G.30, A:T.33, A:D.39, A:F.40, A:R.41, A:R.41, A:R.41, A:S.42, A:Q.111, A:G.178, A:E.179, A:T.203, A:S.204, A:S.204, A:L.205, A:E.208, A:N.227, A:R.228, A:R.228, A:D.229, A:D.248, A:V.249 Water bridges: A:Q.111, A:N.112, A:D.229 Salt bridges: A:R.41 pi-Cation interactions: A:R.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fenwick, M.K. et al., Crystal structure of human sirtuin 3 fragment (residues 118-399) bound to intermediates from reaction with NAD and inhibitor NH6-10. To Be Published

Release Date

2024-08-07

Peptides

NAD-dependent protein deacetylase sirtuin-3, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NAD-dependent protein deacetylase sirtuin-3, mitochondrial

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