SMTL ID : 6h2u.1

Crystal structure of human METTL5-TRMT112 complex, the 18S rRNA m6A1832 methyltransferase at 1.6A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-mer

Ligands

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

SAM.1: 22 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, N.126, P.128, F.141 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Q.28, 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 pi-Stacking: A:F.141 pi-Cation interactions: A:Y.29

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

EDO.2: 6 residues within 4Å: Chain A: V.54, S.119, R.150 Chain B: L.8, M.45, K.48 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.150, A:R.150 EDO.3: 8 residues within 4Å: Chain A: L.112, S.113, N.114, M.116, S.117, T.144, E.147, M.148 No protein-ligand interaction detected (PLIP) EDO.4: 2 residues within 4Å: Chain A: T.46, Y.47 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.47 EDO.7: 5 residues within 4Å: Chain B: R.14, V.49, E.50, W.51, S.52 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.14, B:W.51, B:S.52, B:S.52 Water bridges: B:V.49, B:W.51 EDO.8: 6 residues within 4Å: Chain B: H.12, V.13, R.14, S.18, R.19, G.20 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.14, B:G.20 Water bridges: B:G.15, B:G.15, B:G.17, B:S.18

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

SO4.5: 4 residues within 4Å: Chain A: T.151, R.206, S.208, H.211 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.208 Water bridges: A:K.175, A:K.175, A:R.206, A:F.209 Salt bridges: A:R.206, A:H.211 SO4.6: 3 residues within 4Å: Chain A: K.175, H.210, H.211 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.211 Water bridges: A:K.175 Salt bridges: A:K.175, A:H.210, A:H.211

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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