3PZS

Crystal Structure of a pyridoxamine kinase from Yersinia pestis CO92


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.201
  • R-Value Work: 0.170

Literature

Macromolecules
Sequence Display for 3PZS

Classification: TRANSFERASE

Total Structure Weight: 64527.21

Macromolecule Entities
Molecule Chains Length Organism Details
Pyridoxamine kinase A, B 289 Yersinia pestis EC#: 2.7.1.35 IUBMB
Gene Name(s): pdxY YPO2368 y1967 YP_2154
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BME
Query on BME

A, B BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
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, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 67.91 α = 90.00
b = 88.10 β = 90.00
c = 102.92 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-12-14
  • Released Date: 2011-03-16
  • Deposition author(s): Brunzelle, J.S., Wawrzak, Z., Kudritska, M., Onopriyenko, O., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History

  • Version 1_0: 2011-03-16

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance