SMTL ID : 8d59.1

Crystal structure of human METTL1 in complex with SAM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

monomer

Ligands

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 17 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 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.81, A:I.105, A:R.106, A:N.137, A:A.138, A:M.139, A:T.235, A:E.236, A:E.237 Water bridges: A:R.106, A:L.157 Salt bridges: A:D.160

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: R.106, V.107, K.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.107, A:K.108

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

SO4.3: 4 residues within 4Å: Chain A: K.148, R.255, Q.257, Q.262 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.257, A:Q.262 Salt bridges: A:K.148, A:R.255 SO4.6: 2 residues within 4Å: Chain A: Y.84, R.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.84 Water bridges: A:R.106 Salt bridges: A:R.106

1 x CAC: CACODYLATE ION(Non-covalent)

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

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

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

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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