SMTL ID : 6wuf.1

Crystal structure of mouse DXO in complex with 3'-FADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x UBG: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name)(Non-covalent)

UBG.1: 16 residues within 4Å: Chain A: R.115, E.117, W.151, R.152, G.153, H.154, E.186, R.194, M.205, Y.209, S.252, G.253, Q.254, Q.273, K.275, Q.300 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:E.186 Hydrogen bonds: A:R.115, A:E.117, A:G.153, A:Y.209, A:S.252, A:Q.254, A:Q.254, A:Q.273, A:Q.300, A:Q.300 Water bridges: A:R.78, A:R.78, A:R.78, A:R.78, A:E.121, A:R.122, A:R.152, A:H.154, A:E.184, A:E.184, A:R.197, A:R.197, A:Y.209, A:T.232, A:K.275 Salt bridges: A:R.152, A:R.152, A:K.275

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: Y.90, N.259, V.272, H.308, V.310, T.325 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.308 Water bridges: A:Y.90, A:N.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Doamekpor, S.K. et al., DXO/Rai1 enzymes remove 5'-end FAD and dephospho-CoA caps on RNAs. Nucleic Acids Res. (2020)

Release Date

2020-05-20

Peptides

Decapping and exoribonuclease protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Decapping and exoribonuclease protein

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