› 3run

X-ray diffraction
1.4Å resolution

New strategy to analyze structures of glycopeptide antibiotic-target complexes

Released:
DOI: 10.2210/pdb3run/pdb
PDB entry 3run coloured by chain, front view.
PDB entry 3run coloured by chain, side view.
PDB entry 3run coloured by chain, top view.
Source organisms:
Primary publication:
A carrier protein strategy yields the structure of dalbavancin.
Economou NJ, Nahoum V, Weeks SD, Grasty KC, Zentner IJ, Townsend TM, Bhuiya MW, Cocklin S, Loll PJ
J Am Chem Soc 134 4637-45 (2012)
PMID: 22352468

Function and Biology Details

Reaction catalysed: 
Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133027 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Endolysin Chain: A
Molecule details ›
Chain: A
Length: 168 amino acids
Theoretical weight: 19.02 KDa
Source organism: Tequatrovirus T4
Expression system: Escherichia coli
UniProt:
  • Canonical: P00720 (Residues: 1-164; Coverage: 100%)
Gene name: E
Sequence domains: Phage lysozyme
Structure domains: Lysozyme
VANCOMYCIN Chain: B
Molecule details ›
Chain: B
Length: 7 amino acids
Theoretical weight: 1.15 KDa
Source organism: Amycolatopsis orientalis

Ligands and Environments

Carbohydrate polymer : NEW Components: BGC, RER
Carbohydrate polymer
6 bound ligands:
Ligand MPD 1 x MPD
Ligand MRD 2 x MRD
Ligand PO4 1 x PO4
Ligand TRS 1 x TRS
Ligand CL 1 x CL
Ligand IPA 2 x IPA
4 modified residues:
Ligand CCS 1 x CCS
Ligand DAL 2 x DAL
Ligand GHP 2 x GHP
Ligand OMY 1 x OMY

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X6A
Spacegroup: P3221
Unit cell:
a: 60.44Å b: 60.44Å c: 96.83Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.149 0.148 0.18
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Applications of Nonenzymatic Catalysts to the Alteration of Natural Products.
Shugrue et al. (2017)
5 more

2 mentions without citation

A carrier protein strategy yields the structure of dalbavancin.
Economou et al. (2012)
1 more