PDBe 1rrv

X-ray diffraction
2Å resolution

X-ray crystal structure of TDP-vancosaminyltransferase GtfD as a complex with TDP and the natural substrate, desvancosaminyl vancomycin.

Released:

Function and Biology Details

Reaction catalysed:
dTDP-beta-L-vancosamine + devancosaminyl-vancomycin = dTDP + vancomycin
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Devancosaminyl-vancomycin vancosaminetransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 416 amino acids
Theoretical weight: 43.91 KDa
Source organism: Amycolatopsis orientalis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9AFC7 (Residues: 1-408; Coverage: 100%)
Gene name: gtfD
Sequence domains: Glycosyltransferase family 28 N-terminal domain
Structure domains: Glycogen Phosphorylase B;
DESVANCOSAMINYL VANCOMYCIN Chains: C, D
Molecule details ›
Chains: C, D
Length: 7 amino acids
Theoretical weight: 1.15 KDa
Source organism: Amycolatopsis orientalis

Ligands and Environments


2 modified residues:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 5ID-B
Spacegroup: P21
Unit cell:
a: 50.67Å b: 64.12Å c: 144.08Å
α: 90° β: 91.73° γ: 90°
R-values:
R R work R free
0.21 0.21 0.252
Expression system: Escherichia coli BL21(DE3)