SMTL ID : 6wre.1

Crystal structure of mouse DXO in complex with 5'-OH RNA substrate mimic and calcium ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x U- U37- U37- U- U: RNA (5'-R(*UP*(U37)P*(U37)P*UP)-3')(Non-covalent)

U-U37-U37-U-U.1: 29 residues within 4Å: Chain A: R.52, R.89, E.95, R.96, H.99, W.125, R.126, G.127, H.128, L.175, L.178, M.179, G.182, Y.183, E.186, T.206, S.226, G.227, E.228, E.247, L.248, K.249, T.250, S.251, K.252, K.267, Q.274, R.288 Ligands: CA.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.178, A:G.182, A:Y.183, A:K.249, A:Q.274 Water bridges: A:T.250

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: E.186, D.230, E.247, L.248 Ligands: U-U37-U37-U-U.1, U-U37-U37-U-U.1 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.5

1 x U3P: 3'-URIDINEMONOPHOSPHATE(Non-covalent)

U3P.3: 6 residues within 4Å: Chain A: R.24, T.25, Q.26, G.352, G.353, P.354 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.25, A:T.25, A:Q.26, A:G.352

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Doamekpor, S.K. et al., A novel 5'-hydroxyl dinucleotide hydrolase activity for the DXO/Rai1 family of enzymes. Nucleic Acids Res. (2020)

Release Date

2020-05-13

Peptides

Decapping and exoribonuclease protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Decapping and exoribonuclease protein

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