3TYK

Crystal structure of aminoglycoside phosphotransferase APH(4)-Ia


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.157

Literature

Macromolecules
Sequence Display for 3TYK

Classification: TRANSFERASE / ANTIBIOTIC

Total Structure Weight: 41503.21

Macromolecule Entities
Molecule Chains Length Organism Details
Hygromycin-B 4-O-kinase A 362 Escherichia coli EC#: 2.7.1.163 IUBMB
Gene Name(s): hph
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HY0
Query on HY0

A HYGROMYCIN B VARIANT
6,,4S (Synonym)
C20 H37 N3 O13
GRRNUXAQVGOGFE-XFOBNZBXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET
CSX
Query on CSX
A L-PEPTIDE LINKING C3 H7 N O3 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.157
  • Space Group: P 32 2 1

Unit Cell:

Length (Å) Angle (°)
a = 70.64 α = 90.00
b = 70.64 β = 90.00
c = 125.88 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-09-26
  • Released Date: 2011-10-12
  • Deposition author(s): Stogios, P.J., Shabalin, I.G., Shakya, T., Evdokmova, E., Fan, Y., Chruszcz, M., Minor, W., Wright, G.D., Savchenko, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)
  • Previous versions: 3OVC

Revision History

  • 2012-04-25
    Type: Structure summary
  • 2012-05-02
    Type: Other
  • 2012-11-28
    Type: Structure summary