› 3rum

X-ray diffraction
1.85Å resolution

New strategy to analyze structures of glycopeptide antibiotic-target complexes

Released:
DOI: 10.2210/pdb3rum/pdb
PDB entry 3rum coloured by chain, front view.
PDB entry 3rum coloured by chain, side view.
PDB entry 3rum 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

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142623 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
Maltose/maltodextrin-binding periplasmic protein Chain: A
Molecule details ›
Chain: A
Length: 378 amino acids
Theoretical weight: 41.34 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AEX9 (Residues: 27-392; Coverage: 99%)
Gene names: JW3994, b4034, malE
Sequence domains: Bacterial extracellular solute-binding protein
Structure domains: Periplasmic binding protein-like II
Ristocetin Chains: B, C
Molecule details ›
Chains: B, C
Length: 7 amino acids
Theoretical weight: 1.18 KDa
Source organism: Amycolatopsis lurida

Ligands and Environments

Carbohydrate polymer : NEW Components: MAN, BGC, BXY, RAM
Carbohydrate polymer
Carbohydrate polymer : NEW Components: GLC
Carbohydrate polymer
4 bound ligands:
Ligand IPA 3 x IPA
Ligand SO4 4 x SO4
Ligand RST 2 x RST
Ligand MAN 2 x MAN
5 modified residues:
Ligand CCS 1 x CCS
Ligand DAL 2 x DAL
Ligand GHP 6 x GHP
Ligand OMX 2 x OMX
Ligand MDF 2 x MDF

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X6A
Spacegroup: P212121
Unit cell:
a: 57.833Å b: 75.005Å c: 90.778Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.176 0.219
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

1 mention without citation

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