SMTL ID : 9b0i.1

Cryo-EM Structure of Sf9 produced recombinant N-acetyltransferase 10 (NAT10) in complex with cytidine-amide-CoA bisubstrate probe and ADP/Mg2+.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.1: 16 residues within 4Å: Chain A: G.130, L.268, R.270, Q.274, A.299, G.301, R.302, G.303, K.304, S.305, A.306, T.335, F.339, I.491, R.492 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.130, A:L.268, A:R.270, A:Q.274, A:A.299, A:G.301, A:R.302, A:G.303, A:K.304, A:S.305, A:T.335, A:R.492, A:R.492 Salt bridges: A:K.304 pi-Stacking: A:F.339, A:F.339 ADP.4: 16 residues within 4Å: Chain B: G.130, L.268, R.270, Q.274, A.299, G.301, R.302, G.303, K.304, S.305, A.306, T.335, F.339, I.491, R.492 Ligands: MG.5 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.130, B:L.268, B:R.270, B:Q.274, B:A.299, B:G.301, B:R.302, B:G.303, B:K.304, B:S.305, B:T.335, B:R.492, B:R.492 Salt bridges: B:K.304 pi-Stacking: B:F.339, B:F.339

2 x MG: MAGNESIUM ION

MG.2: 4 residues within 4Å: Chain A: S.305, D.402, E.403 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.305 MG.5: 4 residues within 4Å: Chain B: S.305, D.402, E.403 Ligands: ADP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.305

2 x 01: [[(2~{R},3~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[2-[[1-[(2~{R},3~{S},4~{R},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-2-oxidanylidene-pyrimidin-4-yl]amino]-2-oxidanylidene-ethyl]sulfanylethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate

01.3: 19 residues within 4Å: Chain A: V.649, R.650, I.651, T.653, M.658, S.659, M.660, G.661, G.663, S.664, S.739, Y.740, Q.745, L.746, K.748, F.749, W.750, R.752, T.768 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.746 Hydrogen bonds: A:T.653, A:T.653, A:S.659, A:G.661, A:Y.662, A:G.663, A:S.664, A:S.739, A:T.768 Salt bridges: A:K.748, A:R.752 01.6: 19 residues within 4Å: Chain B: V.649, R.650, I.651, T.653, M.658, S.659, M.660, G.661, G.663, S.664, S.739, Y.740, Q.745, L.746, K.748, F.749, W.750, R.752, T.768 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.746 Hydrogen bonds: B:T.653, B:T.653, B:S.659, B:G.661, B:Y.662, B:G.663, B:S.664, B:S.739, B:T.768 Salt bridges: B:K.748, B:R.752

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, M. et al., Molecular Basis for RNA Cytidine Acetylation by NAT10. Biorxiv (2024)

Release Date

2024-09-11

Peptides

RNA cytidine acetyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

RNA cytidine acetyltransferase

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