SMTL ID : 6trq.1 (1 other biounit)

S.c. Scavenger Decapping Enzyme DcpS in complex with the capped RNA dinucleotide m7G-GU

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.94 Å

Oligo State

homo-dimer

Ligands

1 x 2PO: PHOSPHONATE(Non-covalent)

2PO.1: 5 residues within 4Å: Chain A: D.17, N.19, V.24 Ligands: U.2, 0G.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.17, A:N.19

1 x U: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U.2: 10 residues within 4Å: Chain A: D.17, N.19, F.127, G.275, N.276 Chain B: R.250, I.269, K.270 Ligands: 2PO.1, 0G.3 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.127 Hydrogen bonds: A:N.19, A:N.276, A:N.276, B:R.250, B:I.269

1 x 0G: L-GUANOSINE-5'-MONOPHOSPHATE(Covalent)

0G.3: 14 residues within 4Å: Chain A: V.24, E.41, K.107, N.109, K.121, Y.122, K.191, S.258, Y.259, L.274, S.277 Ligands: 2PO.1, U.2, M7G.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.109, A:S.258 Salt bridges: A:E.41, A:K.121, A:K.191

1 x M7G: 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE(Non-covalent)

M7G.4: 21 residues within 4Å: Chain A: K.121, W.156, I.160, E.166, L.187, P.188, D.189, M.190, K.191, V.203, H.254, P.257, S.258, Y.259, N.263, H.265, K.282 Chain B: N.86, Y.89, W.91 Ligands: 0G.3 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:P.188, A:M.190, A:K.191, A:S.258, A:S.258, A:S.258, A:Y.259, A:N.263, B:N.86 Salt bridges: A:K.121, A:E.166, A:D.189, A:K.191, A:H.254, A:H.254, A:H.265, A:H.265, A:K.282 pi-Stacking: A:W.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fuchs, A.L. et al., Molecular basis of the selective processing of short mRNA substrates by the DcpS mRNA decapping enzyme. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-07-22

Peptides

m7GpppX diphosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

m7GpppX diphosphatase

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