1DGM

CRYSTAL STRUCTURE OF ADENOSINE KINASE FROM TOXOPLASMA GONDII

Structural Biology Knowledgebase: 1DGM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.214

Literature

Macromolecules
Sequence Display for 1DGM

Classification: TRANSFERASE

Total Structure Weight: 38812.23

Macromolecule Entities
Molecule Chains Length Organism Details
ADENOSINE KINASE A 363 Toxoplasma gondii EC#: 2.7.1.20 IUBMB
Mutation: L179F
Gene Name(s): AK
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ADN
Query on ADN

A ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACY
Query on ACY

A ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-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)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ADN Ki: 8900 nM (99) BindingDB

N/A in BindingMoad
Ki: 8900 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.214
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 47.55 α = 90.00
b = 68.75 β = 100.30
c = 57.29 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-11-24
  • Released Date: 2000-11-29
  • Deposition author(s): Cook, W.J., DeLucas, L.J., Chattopadhyay, D.

Revision History

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