SMTL ID : 8d5b.1

Crystal structure of human METTL1 in complex with SAH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

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

SAH.1: 18 residues within 4Å: Chain A: G.81, C.82, G.83, L.103, E.104, I.105, R.106, S.136, N.137, A.138, M.139, L.157, F.158, D.160, T.235, E.236, E.237 Ligands: GOL.7 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.81, A:G.83, A:I.105, A:N.137, A:A.138, A:M.139, A:E.237 Water bridges: A:L.157, A:L.157, A:D.160, A:E.236

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: K.148, V.187, R.255, Q.257 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.257 Water bridges: A:D.258 Salt bridges: A:K.148, A:R.255 SO4.6: 4 residues within 4Å: Chain A: Y.84, R.106, K.108 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.106, A:K.108

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: R.106, V.107, K.108 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.106, A:V.107, A:K.108 GOL.7: 7 residues within 4Å: Chain A: Y.84, R.106, V.109, E.236, E.237 Ligands: SAH.1, SO4.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.106, A:R.106, A:E.237

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: Y.84, G.85, G.86, T.235, E.236 Ligand excluded by PLIP

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.5: 3 residues within 4Å: Chain A: K.240, R.243, N.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.243, A:R.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruiz-Arroyo, V.M. et al., Structures and mechanisms of tRNA methylation by METTL1-WDR4. Nature (2023)

Release Date

2023-01-11

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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