› 1ob5

X-ray diffraction
3.1Å resolution

T. aquaticus elongation factor EF-Tu complexed with the antibiotic enacyloxin IIa, a GTP analog, and Phe-tRNA

Released:
DOI: 10.2210/pdb1ob5/pdb
PDB entry 1ob5 coloured by chain, front view.
PDB entry 1ob5 coloured by chain, side view.
PDB entry 1ob5 coloured by chain, top view.
Source organisms:
Primary publication:
Enacyloxin IIa pinpoints a binding pocket of elongation factor Tu for development of novel antibiotics.
Parmeggiani A, Krab IM, Watanabe T, Nielsen RC, Dahlberg C, Nyborg J, Nissen P
J Biol Chem 281 2893-900 (2006)
PMID: 16257965

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-169615 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Elongation factor Tu Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 405 amino acids
Theoretical weight: 44.74 KDa
Source organism: Thermus aquaticus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q01698 (Residues: 2-406; Coverage: 100%)
Gene names: tuf, tufA
Sequence domains:
Structure domains:
TRANSFER-RNA, PHE Chains: B, D, F
Molecule details ›
Chains: B, D, F
Length: 78 nucleotides
Theoretical weight: 25.33 KDa
Source organism: Saccharomyces cerevisiae
Sequence domains: tRNA

Ligands and Environments

3 bound ligands:
Ligand GNP 3 x GNP
Ligand MG 3 x MG
Ligand ENX 3 x ENX
12 modified residues:
Ligand 2MG 3 x 2MG
Ligand H2U 6 x H2U
Ligand M2G 3 x M2G
Ligand OMC 3 x OMC
Ligand OMG 3 x OMG
Ligand YG 3 x YG
Ligand PSU 6 x PSU
Ligand 5MC 6 x 5MC
Ligand 7MG 3 x 7MG
Ligand 5MU 3 x 5MU
Ligand 1MA 3 x 1MA
Ligand PHA 3 x PHA

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X13
Spacegroup: C2
Unit cell:
a: 212.57Å b: 122.33Å c: 135.68Å
α: 90° β: 121.3° γ: 90°
R-values:
R R work R free
0.28 0.28 0.294
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

9 review citations

New antibiotics from bacterial natural products.
Clardy et al. (2006)
8 more

6 mentions without citation

Pathways to disease from natural variations in human cytoplasmic tRNAs.
Lant et al. (2019)
5 more