SMTL ID : 8z62.1 (1 other biounit)

Crystal structure of rRNA (uracil-C5)-methyltransferase from Pyrococcus horikoshii OT3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

monomer

Ligands

1 x NA: SODIUM ION(Non-functional Binders)

NA.1: 6 residues within 4Å: Chain A: I.136, P.140, I.141, F.142, S.143, T.146 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.142, A:S.143, A:T.146, A:T.146

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

SO4.2: 2 residues within 4Å: Chain A: R.38, R.40 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.38, A:R.40 SO4.3: 5 residues within 4Å: Chain A: K.125, E.126, F.127, G.128, K.131 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.128 Salt bridges: A:K.125, A:K.131

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

EDO.4: 3 residues within 4Å: Chain A: T.94, G.95, I.96 No protein-ligand interaction detected (PLIP) EDO.5: 1 residues within 4Å: Chain A: W.167 No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain A: K.358, G.360, R.411 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.360

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

PEG.7: 7 residues within 4Å: Chain A: T.118, N.120, G.121, I.122, G.123, V.134, R.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.135 PEG.8: 3 residues within 4Å: Chain A: G.61, S.64, H.65 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.65 Water bridges: A:L.51, A:M.52 PEG.9: 3 residues within 4Å: Chain A: Q.75, W.107, P.140 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saha, S. et al., Decoding Substrate Selectivity of an Archaeal RlmCD-like Methyltransferase Through Its Salient Traits. Biochemistry (2024)

Release Date

2024-10-16

Peptides

23S rRNA (uracil(747)-C(5))-methyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

23S rRNA (uracil(747)-C(5))-methyltransferase

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