SMTL ID : 5zw3.1

Crystal Structure of TrmR from B. subtilis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 20 residues within 4Å: Chain A: P.36, I.37, M.38, E.60, G.62, T.63, A.64, Y.67, S.68, E.85, R.86, N.87, R.90, G.112, D.113, A.114, D.133, A.134, A.135, F.142 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.64 Hydrogen bonds: A:M.38, A:A.64, A:Y.67, A:S.68, A:S.68, A:R.86, A:R.90, A:D.113, A:A.114, A:D.133, A:D.133, A:A.135 Water bridges: A:T.63, A:R.90 SAH.3: 19 residues within 4Å: Chain B: P.36, I.37, M.38, G.62, T.63, A.64, Y.67, S.68, E.85, R.86, N.87, R.90, G.112, D.113, A.114, D.133, A.134, A.135, F.142 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.64 Hydrogen bonds: B:M.38, B:A.64, B:Y.67, B:S.68, B:S.68, B:R.86, B:R.90, B:R.90, B:D.113, B:A.114, B:D.133, B:D.133, B:A.135 Water bridges: B:R.90

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.133, D.159, N.160 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.133, A:D.159, H2O.1, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain B: D.133, D.159, N.160 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.133, B:D.159, H2O.2, H2O.3, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ryu, H. et al., Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine. Nucleic Acids Res. (2018)

Release Date

2018-07-11

Peptides

Putative O-methyltransferase YrrM: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative O-methyltransferase YrrM

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