SMTL ID : 7dpe.1

RNA methyltransferase METTL4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 21 residues within 4Å: Chain A: I.141, S.210, D.211, L.212, D.233, P.235, Y.247, P.248, L.250, S.362, R.363, K.364, E.385, F.387, R.389, W.398, N.400, E.401, F.405 Ligands: GOL.3, GOL.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:R.389 Hydrogen bonds: A:D.211, A:L.212, A:D.233, A:D.233, A:K.364, A:E.385, A:N.400, A:N.400, A:E.401 Water bridges: A:R.389, A:R.389, A:E.401 Salt bridges: A:K.364, A:R.389 SAH.6: 21 residues within 4Å: Chain B: I.141, S.210, D.211, L.212, D.233, P.235, Y.247, P.248, L.250, S.362, R.363, K.364, E.385, F.387, R.389, W.398, N.400, E.401, F.405 Ligands: GOL.8, GOL.9 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:R.389 Hydrogen bonds: B:D.211, B:L.212, B:D.233, B:K.364, B:N.400, B:N.400, B:E.401, B:E.401 Water bridges: B:R.389, B:R.389, B:E.401 Salt bridges: B:K.364, B:R.389

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: P.365, P.366, I.367, G.368, E.385, A.392, W.395 Ligands: GOL.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.365, A:I.367, A:E.385 GOL.3: 7 residues within 4Å: Chain A: W.274, K.364, P.365, E.385, E.390 Ligands: SAH.1, GOL.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.233, A:P.365, A:E.390 Water bridges: A:R.363 GOL.4: 5 residues within 4Å: Chain A: D.211, L.212, H.213, Y.254 Ligands: SAH.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.211, A:L.212 GOL.5: 5 residues within 4Å: Chain A: K.246, Y.247, R.389, E.401, H.404 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.389, A:R.389 GOL.7: 8 residues within 4Å: Chain B: P.365, P.366, I.367, G.368, E.385, A.392, W.395 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.365, B:I.367, B:E.385 GOL.8: 7 residues within 4Å: Chain B: W.274, K.364, P.365, E.385, E.390 Ligands: SAH.6, GOL.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.365, B:E.390 Water bridges: B:R.363, B:E.390 GOL.9: 5 residues within 4Å: Chain B: D.211, L.212, H.213, Y.254 Ligands: SAH.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.211, B:L.212 GOL.10: 5 residues within 4Å: Chain B: K.246, Y.247, R.389, E.401, H.404 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.389, B:R.389

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luo, Q. et al., Structure of RNA m6A methyltransferase METTL4 in complex with DNA at 2.75 Angstroms resolutioon. To Be Published

Release Date

2021-12-22

Peptides

Methyltransferase-like protein 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Methyltransferase-like protein 2

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