2DDM

Crystal Structure of Pyridoxal Kinase from the Escherichia coli PdxK gene at 2.1 A resolution

Structural Biology Knowledgebase: 2DDM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.194

Literature

Macromolecules
Sequence Display for 2DDM

Classification: TRANSFERASE

Total Structure Weight: 61997.35

Macromolecule Entities
Molecule Chains Length Organism Details
Pyridoxine kinase A, B 283 Escherichia coli EC#: 2.7.1.35 IUBMB
Gene Name(s): pdxK yfeI b2418 JW2411
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.194
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 65.31 α = 90.00
b = 75.13 β = 90.00
c = 107.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-02-02
  • Released Date: 2006-08-15
  • Deposition author(s): Safo, M.K., Musayev, F.N., di Salvo, M.L., Hunt, S., Claude, J.B., Schirch, V.

Revision History

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