3GBZ | pdb_00003gbz

Structure of the CMGC CDK Kinase from Giardia lamblia

• PDB DOI: https://doi.org/10.2210/pdb3GBZ/pdb

• Classification: TRANSFERASE
• Organism(s): Giardia lamblia ATCC 50803
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-20 Released: 2009-03-24 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.236 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Structure of a cyclin-dependent kinase from Giardia lamblia.

Leibly, D.J., Newling, P.A., Abendroth, J., Guo, W., Kelley, A., Stewart, L.J., Van Voorhis, W.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1084-1089

• PubMed: 21904054 
• DOI: https://doi.org/10.1107/S1744309111018070
• Primary Citation Related Structures: 
  3GBZ, 3GC0


• PubMed Abstract: 
  

  Giardia lamblia is the etiologic agent of giardiasis, a water-borne infection that is prevalent throughout the world. The need for new therapeutics for the treatment of giardiasis is of paramount importance. Owing to the ubiquitous nature of kinases and their vital importance in organisms, they are potential drug targets. In this paper, the first structure of a cyclin-dependent kinase (CDK) from G. lamblia (GlCDK; UniProt A8BZ95) is presented. CDKs are cell-cycle-associated kinases that are actively being pursued as targets for anticancer drugs as well as for antiparasitic chemotherapy. Generally, a CDK forms a complex with its associated cyclin. This CDK-cyclin complex is active and acts as a serine/threonine protein kinase. Typically, CDKs are responsible for the transition to the next phase of the cell cycle. Although the structure of GlCDK with its associated cyclin was not solved, the 1.85 Å resolution structure of apo GlCDK and a 2.0 Å resolution structure of GlCDK in complex with adenosine monophosphate are presented and the structural differences from the orthologous human CDK2 and CDK3 are discussed.

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Organizational Affiliation: 
• Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.58 kDa 
• Atom Count: 2,397 
• Modeled Residue Count: 274 
• Deposited Residue Count: 329 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinase, CMGC CDK	A	329	Giardia lamblia ATCC 50803	Mutation(s): 0  Gene Names: GL50803_8037 EC: 2.7.11.22
UniProt
Find proteins for A8BZ95 (Giardia intestinalis (strain ATCC 50803 / WB clone C6)) Explore A8BZ95  Go to UniProtKB:  A8BZ95

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.236 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33GBZ

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.72	α = 90
b = 73.05	β = 90
c = 75.01	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-24 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2011-09-21
  Changes: Database references
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description