2DFN

Structure of shikimate kinase from Mycobacterium tuberculosis complexed with ADP and shikimate at 1.9 angstrons of resolution

Structural Biology Knowledgebase: 2DFN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.267
  • R-Value Work: 0.202

Literature

Macromolecules
Sequence Display for 2DFN

Classification: TRANSFERASE

Total Structure Weight: 19249.30

Macromolecule Entities
Molecule Chains Length Organism Details
Shikimate kinase A 176 Mycobacterium tuberculosis EC#: 2.7.1.71 IUBMB
Gene Name(s): aroK Rv2539c MTCY159.17
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SKM
Query on SKM

A (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE- 1-CARBOXYLIC ACID
SHIKIMATE (Synonym)
C7 H10 O5
JXOHGGNKMLTUBP-HSUXUTPPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.267
  • R-Value Work: 0.202
  • Space Group: P 32 2 1

Unit Cell:

Length (Å) Angle (°)
a = 63.30 α = 90.00
b = 63.30 β = 90.00
c = 91.61 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-03-03
  • Released Date: 2006-09-03
  • Deposition author(s): Dias, M.V., Faim, L.M., Vasconcelos, I.B., de Oliveira, J.S., Basso, L.A., Santos, D.S., de Azevedo, W.F.

Revision History

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