SMTL ID : 7pl1.1

Crystal structure of human METTL1 bound to Sinefungin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: I.95, R.125, S.126, N.127, H.131 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.125, A:R.125, A:N.127, A:N.127 Water bridges: A:S.126, A:H.131 GOL.2: 3 residues within 4Å: Chain A: R.96, V.97, K.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.96, A:V.97, A:K.98 GOL.6: 9 residues within 4Å: Chain A: P.28, W.33, F.41, Q.64, V.65, F.135, F.136, Y.137, Q.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.65, A:Q.140

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 3 residues within 4Å: Chain A: K.138, L.203, R.245 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.138, A:R.245, A:R.245 Water bridges: A:K.138 PEG.4: 4 residues within 4Å: Chain A: Y.74, Y.102, R.106 Ligands: PEG.5 No protein-ligand interaction detected (PLIP) PEG.5: 9 residues within 4Å: Chain A: Y.74, G.75, G.76, R.106, S.224, T.225, E.226, K.229 Ligands: PEG.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.74, A:G.76, A:E.80, A:R.106, A:R.106, A:E.226, A:K.229

1 x SFG: SINEFUNGIN(Non-covalent)

SFG.7: 15 residues within 4Å: Chain A: G.71, C.72, G.73, L.93, E.94, I.95, R.96, S.126, N.127, A.128, M.129, L.147, F.148, T.225, E.227 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.71, A:G.73, A:I.95, A:N.127, A:A.128, A:M.129, A:E.227, A:E.227 Water bridges: A:L.147, A:L.147, A:D.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nai, F. et al., Small-Molecule Inhibitors of the m7G-RNA Writer METTL1. Acs Bio Med Chem Au (2023)

Release Date

2021-09-15

Peptides

tRNA (guanine-N(7)-)-methyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

tRNA (guanine-N(7)-)-methyltransferase

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