2I5B

The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parralel emergence of enzyme activity during evolution

Structural Biology Knowledgebase: 2I5B SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.222

Literature

Macromolecules
Sequence Display for 2I5B

Classification: transferase

Total Structure Weight: 147373.02

Macromolecule Entities
Molecule Chains Length Organism Details
Phosphomethylpyrimidine kinase A, B, C, D, E 271 Bacillus subtilis EC#: 2.7.4.7 IUBMB
Gene Name(s): pdxK ywdB BSU38020 ipa-52r
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D, E ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.222
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 102.50 α = 90.00
b = 102.50 β = 90.00
c = 251.36 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-08-24
  • Released Date: 2006-09-19
  • Deposition author(s): Newman, J.A., Das, S.K., Sedelnikova, S.E., Rice, D.W.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4