› 4mcb

X-ray diffraction
1.94Å resolution

H.influenzae TrmD in complex with N-(4-{[(1H-IMIDAZOL-2-YLMETHYL)AMINO]METHYL}BENZYL)-4-OXO-3,4-DIHYDROTHIENO[2,3-D]PYRIMIDINE-5-CARBOXAMIDE

Released:
DOI: 10.2210/pdb4mcb/pdb
PDB entry 4mcb coloured by chain, front view.
PDB entry 4mcb coloured by chain, side view.
PDB entry 4mcb coloured by chain, top view.
Source organism: Haemophilus influenzae Rd KW20
Primary publication:
Selective inhibitors of bacterial t-RNA-(N(1)G37) methyltransferase (TrmD) that demonstrate novel ordering of the lid domain.
Hill PJ, Abibi A, Albert R, Andrews B, Gagnon MM, Gao N, Grebe T, Hajec LI, Huang J, Livchak S, Lahiri SD, McKinney DC, Thresher J, Wang H, Olivier N, Buurman ET
J Med Chem 56 7278-88 (2013)
PMID: 23981144

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + guanine(37) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine(37) in tRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155154 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (guanine-N(1)-)-methyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 246 amino acids
Theoretical weight: 27.58 KDa
Source organism: Haemophilus influenzae Rd KW20
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P43912 (Residues: 1-246; Coverage: 100%)
Gene names: HI_0202, trmD
Sequence domains: tRNA (Guanine-1)-methyltransferase
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand GOL 1 x GOL
Ligand SO4 2 x SO4
Ligand 21W 2 x 21W
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: P41
Unit cell:
a: 74.158Å b: 74.158Å c: 119.288Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.178 0.205
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 review citations

tRNA modifications regulate translation during cellular stress.
Gu et al. (2014)
6 more

2 mentions without citation

Combined Approach of Patch-Surfer and PL-PatchSurfer for Protein-Ligand Binding Prediction in CSAR 2013 and 2014.
Zhu et al. (2016)
1 more