3H5Q

Crystal structure of a putative pyrimidine-nucleoside phosphorylase from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.166

Literature

Macromolecules
Sequence Display for 3H5Q

Classification: TRANSFERASE

Total Structure Weight: 47845.88

Macromolecule Entities
Molecule Chains Length Organism Details
Pyrimidine-nucleoside phosphorylase A 436 Staphylococcus aureus EC#: 2.4.2.2 IUBMB
Mutation: A56V
Gene Name(s): pdp pyn SACOL2128
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A THYMIDINE
DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE (Synonym)
C10 H14 N2 O5
IQFYYKKMVGJFEH-XLPZGREQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 51.59 α = 90.00
b = 40.88 β = 97.19
c = 105.58 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-04-22
  • Released Date: 2009-05-26
  • Deposition author(s): Shumilin, I.A., Zimmerman, M., Cymborowski, M., Skarina, T., Onopriyenko, O., Anderson, W.F., Savchenko, A., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History

  • Version 1_0: 2009-05-26

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Advisory, Version format compliance