3ZCW | pdb_00003zcw

Eg5 - New allosteric binding site

• PDB DOI: https://doi.org/10.2210/pdb3ZCW/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-11-23 Released: 2013-01-23 
• Deposition Author(s): Ulaganathan, V., Talapatra, S.K., Kozielski, F., Pannifer, A.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.233 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Structural Insights Into a Unique Inhibitor Binding Pocket in Kinesin Spindle Protein.

Ulaganathan, V., Talapatra, S.K., Rath, O., Pannifer, A.D., Hackney, D.D., Kozielski, F.

(2013) J Am Chem Soc 135: 2263

• PubMed: 23305346 
• DOI: https://doi.org/10.1021/ja310377d
• Primary Citation Related Structures: 
  3ZCW


• PubMed Abstract: 
  

  Human kinesin Eg5 is a target for drug development in cancer chemotherapy with compounds in phase II clinical trials. These agents bind to a well-characterized allosteric pocket involving the loop L5 region, a structural element in kinesin-5 family members thought to provide inhibitor specificity. Using X-ray crystallography, kinetic, and biophysical methods, we have identified and characterized a distinct allosteric pocket in Eg5 able to bind inhibitors with nanomolar K(d). This pocket is formed by key structural elements thought to be pivotal for force generation in kinesins and may represent a novel site for therapeutic intervention in this increasingly well-validated drug target.

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Organizational Affiliation: 
• The Molecular Motors Laboratory, The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland, UK.

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: 40.52 kDa 
• Atom Count: 3,129 
• Modeled Residue Count: 321 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KINESIN-LIKE PROTEIN KIF11	A	348	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P52732 (Homo sapiens) Explore P52732  Go to UniProtKB:  P52732
PHAROS:  P52732 GTEx:  ENSG00000138160

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4A2	D [auth A], E [auth A]	(2E)-2-(3-fluoranyl-4-methoxy-phenyl)imino-1-[[2-(trifluoromethyl)phenyl]methyl]-3H-benzimidazole-5-carboxylic acid C23 H17 F4 N3 O3 KSDBWRGNYBMBEZ-UHFFFAOYSA-N
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
EPE	F [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
PEG	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.233 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.94	α = 90
b = 62.89	β = 117.46
c = 75.05	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Ulaganathan, V., Talapatra, S.K., Kozielski, F., Pannifer, A.D.

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2013-01-30
  Changes: Structure summary
• Version 1.2: 2013-02-27
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description