SMTL ID : 8joz.1

Crystal structure of CmoM from E. coli complexed with sinefungin and cellularly expressed tRNA Ser

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

monomer

Ligands

1 x SFG: SINEFUNGIN(Non-covalent)

SFG.1: 21 residues within 4Å: Chain A: D.19, R.20, F.22, F.29, Y.34, R.42, G.68, G.69, G.70, D.89, L.90, S.91, M.94, A.117, A.118, Q.119, H.135, A.136, V.137, V.141 Chain B: N.35 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.29 Hydrogen bonds: A:F.22, A:Y.34, A:G.68, A:L.90, A:S.91, A:A.118, A:Q.119, A:Q.119, A:A.136 Water bridges: A:R.42, A:G.69, A:Q.73, A:T.74, A:H.135 Salt bridges: A:R.42

7 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: G.9, C.12 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: U.59, C.60, A.62 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain B: G.46 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain B: A.71 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoo, J. et al., Structural basis for the selective methylation of 5-carboxymethoxyuridine in tRNA modification. Nucleic Acids Res. (2023)

Release Date

2023-08-30

Peptides

tRNA 5-carboxymethoxyuridine methyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

tRNA 5-carboxymethoxyuridine methyltransferase