2ITM

Crystal structure of the E. coli xylulose kinase complexed with xylulose

Structural Biology Knowledgebase: 2ITM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.263
  • R-Value Work: 0.201

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2ITM

Classification: TRANSFERASE

Total Structure Weight: 106047.89

Macromolecule Entities
Molecule Chains Length Organism Details
Xylulose kinase A, B 484 Escherichia coli EC#: 2.7.1.17 IUBMB
Gene Name(s): xylB b3564 JW3536
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B D-XYLULOSE
C5 H10 O5
ZAQJHHRNXZUBTE-WUJLRWPWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NH4
Query on NH4

A, B AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
XUL N/A in BindingDB
Kd: 74000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.263
  • R-Value Work: 0.201
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 61.88 α = 90.00
b = 112.61 β = 90.00
c = 143.07 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-10-19
  • Released Date: 2006-11-14
  • Deposition author(s): di Luccio, E., Voegtli, J., Wilson, D.K.

Revision History

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