SMTL ID : 6h2v.1 (1 other biounit)

Crystal structure of human METTL5-TRMT112 complex, the 18S rRNA m6A1832 methyltransferase at 2.5A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

hetero-1-1-mer

Ligands

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

SAM.1: 20 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, V.64, D.81, I.82, C.107, D.108, V.109, N.126, P.128, F.141 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.28, A:T.31, A:T.31, A:G.59, A:C.62, A:I.82, A:D.108, A:V.109, A:K.132 Water bridges: A:N.126 pi-Stacking: A:F.141 pi-Cation interactions: A:Y.29

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

SO4.2: 6 residues within 4Å: Chain A: T.151, K.175, R.206, S.208, F.209, H.211 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.208, A:F.209, A:F.209 Salt bridges: A:K.175, A:R.206, A:H.211 SO4.3: 3 residues within 4Å: Chain A: K.175, H.210, H.211 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.211 Salt bridges: A:K.175, A:H.210 SO4.4: 4 residues within 4Å: Chain A: R.32, P.187, A.188, S.189 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.188 Salt bridges: A:R.32 SO4.7: 3 residues within 4Å: Chain B: E.36, F.37, R.82 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.37 Salt bridges: B:R.82

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

PEG.5: 6 residues within 4Å: Chain A: E.84, Q.106 Chain B: P.108, S.110, I.113, N.115 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.115, A:E.84

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 4 residues within 4Å: Chain B: I.32, P.34, H.86, E.90 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van Tran, N. et al., The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112. Nucleic Acids Res. (2019)

Release Date

2019-07-31

Peptides

Methyltransferase-like protein 5: A
Multifunctional methyltransferase subunit TRM112-like protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Methyltransferase-like protein 5

Multifunctional methyltransferase subunit TRM112-like protein

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