SMTL ID : 6is0.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

SAH.1: 19 residues within 4Å: Chain A: L.65, 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 Ligands: EDO.6 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:L.321, A:E.338, A:F.340, A:A.341, A:N.345, A:N.345, A:F.368, A:N.381 Water bridges: A:S.320, A:S.320, A:S.342, A:A.354, A:L.369, A:N.381

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

M7G.2: 9 residues within 4Å: Chain A: R.62, R.92, E.93, E.386, W.416, D.418, P.419, P.420, T.421 16 PLIP interactions: 16 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.62, A:R.62, A:R.62, A:R.62, A:E.93 Salt bridges: A:R.62, A:E.386 pi-Stacking: A:W.416, A:W.416, A:W.416, A:W.416

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

EDO.3: 5 residues within 4Å: Chain A: H.21, G.73, L.74, D.75, P.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.21 Water bridges: A:L.74 EDO.4: 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.5: 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 Water bridges: A:R.295 EDO.6: 6 residues within 4Å: Chain A: G.319, N.381, P.382, P.383, F.384 Ligands: SAH.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.381 Water bridges: A:G.319, A:F.384

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.7: 10 residues within 4Å: Chain A: E.15, R.16, A.17, P.18, E.224, V.225, Q.226, D.227, R.228, Y.233 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.15, A:V.225, A:V.225, A:Q.226, A:D.227, A:R.228, A:Y.233, A:Y.233

1 x M7G- A2M- G: m7G-capped RNA(Non-covalent)

M7G-A2M-G.8: 3 residues within 4Å: Chain A: K.108, S.157, K.158 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.108 Hydrogen bonds: A:K.158

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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