SMTL ID : 5uli.1

Crystal Structure of mouse DXO in complex with (3'-NADP)+ and calcium ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.186, D.230, E.247, L.248 Ligands: 0WD.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.230, A:E.247, A:L.248, H2O.1, H2O.1

1 x 0WD: [[(2R,3S,4R,5R)-5-(3-aminocarbonyl-4H-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

0WD.2: 18 residues within 4Å: Chain A: L.48, R.52, R.89, E.91, W.125, R.126, G.127, H.128, E.158, Y.183, C.211, S.226, G.227, E.228, E.247, K.249, Q.274 Ligands: CA.1 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:R.52, A:R.89, A:R.89, A:E.91, A:E.91, A:G.127, A:E.158, A:E.158, A:Y.183, A:E.228, A:E.228, A:E.228, A:E.247, A:Q.274, A:Q.274 Water bridges: A:R.96, A:G.127, A:E.158 Salt bridges: A:R.126, A:R.126, A:K.249 pi-Cation interactions: A:R.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiao, X. et al., 5' End Nicotinamide Adenine Dinucleotide Cap in Human Cells Promotes RNA Decay through DXO-Mediated deNADding. Cell (2017)

Release Date

2017-05-17

Peptides

Decapping and exoribonuclease protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Decapping and exoribonuclease protein

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