› 3rul

X-ray diffraction
2.5Å resolution

New strategy to analyze structures of glycopeptide-target complexes

Released:
DOI: 10.2210/pdb3rul/pdb
PDB entry 3rul coloured by chain, front view.
PDB entry 3rul coloured by chain, side view.
PDB entry 3rul coloured by chain, top view.
Source organism: Homo sapiens
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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143371 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 79 amino acids
Theoretical weight: 8.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-683; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Dalbavancin Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 7 amino acids
Theoretical weight: 1.29 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand TLA 4 x TLA
Ligand CL 1 x CL
Ligand N1L 4 x N1L
Ligand MAN 4 x MAN
Ligand M12 4 x M12
5 modified residues:
Ligand CCS 4 x CCS
Ligand DAL 8 x DAL
Ligand DTY 4 x DTY
Ligand GHP 8 x GHP
Ligand OMY 4 x OMY

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X6A
Spacegroup: P212121
Unit cell:
a: 53.3Å b: 86.25Å c: 107.19Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.244 0.243 0.277
Expression systems:
  • Escherichia coli
  • Not provided

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