SMTL ID : 9ohl.1

TRMT112-METTL5 bound to SAM and FWG-33B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

hetero-1-1-mer

Ligands

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

SAM.1: 23 residues within 4Å: Chain A: F.19, L.26, E.27, Q.28, Y.29, P.30, T.31, G.59, C.60, G.61, C.62, G.63, V.64, L.65, D.81, I.82, C.107, D.108, V.109, C.110, N.126, P.128, F.141 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:Q.28, A:T.31, A:T.31, A:T.31, A:C.60, A:C.62, A:G.63, A:V.64, A:I.82, A:D.108, A:D.108, A:V.109 Water bridges: A:L.65, A:L.65, A:K.132 pi-Stacking: A:F.141 pi-Cation interactions: A:Y.29

1 x 01: N-(4-{[(3aS,4R,6S,6aR)-6-(3-chlorophenyl)-2-propanoyloctahydrocyclopenta[c]pyrrol-4-yl]oxy}phenyl)acetamide

01.2: 14 residues within 4Å: Chain A: V.105, C.107, L.111, L.112, R.115, M.116 Chain B: L.9, C.100, E.102, F.107, M.116, L.117, L.118, S.119 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.111, A:L.111, A:L.112, A:R.115, B:L.9, B:M.116, B:L.117, B:L.118, B:L.118 Hydrogen bonds: A:R.115, B:L.118 Water bridges: A:R.115

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain B: R.44, K.48 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.44, B:K.48, B:K.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goetzke, F.W. et al., Complexoform-restricted covalent TRMT112 ligands that allosterically agonize METTL5. Biorxiv (2025)

Release Date

2025-06-11

Peptides

rRNA N(6)-adenosine-methyltransferase METTL5: A
Multifunctional methyltransferase subunit TRM112-like protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

rRNA N(6)-adenosine-methyltransferase METTL5

Multifunctional methyltransferase subunit TRM112-like protein

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