3VDN

Crystal Structure of VldE, the pseudo-glycosyltransferase, in complex with GDP

Structural Biology Knowledgebase: 3VDN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.286
  • R-Value Work: 0.241

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VDN

Classification: TRANSFERASE

Total Structure Weight: 55450.30

Macromolecule Entities
Molecule Chains Length Organism Details
VldE B 497 Streptomyces hygroscopicus EC#: 2.4 IUBMB

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GDP
Query on GDP

B GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.286
  • R-Value Work: 0.241
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 84.03 α = 90.00
b = 121.04 β = 90.00
c = 47.82 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-01-05
  • Released Date: 2013-01-09
  • Deposition author(s): Cavalier, M.C., Yim, Y.-S., Asamizu, S., Neau, D., Mahmud, T., Lee, Y.-H.

Revision History

No revisions since initial release