SMTL ID : 6irz.1

Crystal structure of the zebrafish cap-specific adenosine methyltransferase bound to SAH and m7G-capped RNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 20 residues within 4Å: Chain A: L.65, Q.318, G.319, S.320, L.321, F.326, E.338, C.339, F.340, A.341, S.342, N.345, C.352, S.353, A.354, P.367, F.368, E.379, N.381, P.383 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:L.321, A:E.338, A:F.340, A:F.340, A:A.341, A:N.345, A:F.368, A:N.381 Water bridges: A:Q.318, A:Q.318, A:L.369, A:N.381

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

EDO.2: 8 residues within 4Å: Chain A: L.64, L.65, K.68, P.76, L.77, M.306, A.354, F.355 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.77 EDO.3: 9 residues within 4Å: Chain A: P.24, H.25, P.26, A.241, P.242, P.243, Q.244, K.291, S.294 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.295 EDO.4: 6 residues within 4Å: Chain A: V.235, R.236, L.237, D.285, R.295, F.361 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.235, A:L.237, A:D.285, A:R.295 Water bridges: A:R.236, A:R.236, A:D.285

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

M7G.5: 10 residues within 4Å: Chain A: R.62, R.92, E.93, E.386, W.416, D.418, P.419, P.420, T.421, H.465 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.92, A:R.92, A:E.386, A:P.419, A:P.420 Water bridges: A:R.92, A:E.93, A:N.96 Salt bridges: A:E.386 pi-Stacking: A:W.416

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Akichika, S. et al., Cap-specific terminal N 6 -methylation of RNA by an RNA polymerase II-associated methyltransferase. Science (2019)

Release Date

2018-12-05

Peptides

PDX1 C-terminal-inhibiting factor 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PDX1 C-terminal-inhibiting factor 1

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