Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.04 kDa 
• Atom Count: 2749 
• Modelled Residue Count: 333 
• Deposited Residue Count: 369 
• Unique protein chains: 1

3KEN

Human Eg5 in complex with S-trityl-L-cysteine

• PDB DOI: 10.2210/pdb3KEN/pdb

• Classification: MOTOR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-10-26 Released: 2010-03-16 
• Deposition Author(s): Parke, C.L., Wojcik, E.J., Kim, S., Worthylake, D.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.275 
• R-Value Work: 0.241 

Literature

Allosteric drug discrimination is coupled to mechanochemical changes in the kinesin-5 motor core.

Kim, E.D., Buckley, R., Learman, S., Richard, J., Parke, C., Worthylake, D.K., Wojcik, E.J., Walker, R.A., Kim, S.

(2010) J Biol Chem 285: 18650-18661

• PubMed: 20299460 
• DOI: 10.1074/jbc.M109.092072
• Primary Citation of Related Structures:  
  3KEN


• PubMed Abstract: 
  

Essential in mitosis, the human Kinesin-5 protein is a target for >80 classes of allosteric compounds that bind to a surface-exposed site formed by the L5 loop. Not established is why there are differing efficacies in drug inhibition. Here we compare the ligand-bound states of two L5-directed inhibitors against 15 Kinesin-5 mutants by ATPase assays and IR spectroscopy. Biochemical kinetics uncovers functional differences between individual residues at the N or C termini of the L5 loop. Infrared evaluation of solution structures and multivariate analysis of the vibrational spectra reveal that mutation and/or ligand binding not only can remodel the allosteric binding surface but also can transmit long range effects. Changes in L5-localized 3(10) helix and disordered content, regardless of substitution or drug potency, are experimentally detected. Principal component analysis couples these local structural events to two types of rearrangements in beta-sheet hydrogen bonding. These transformations in beta-sheet contacts are correlated with inhibitory drug response and are corroborated by wild type Kinesin-5 crystal structures. Despite considerable evolutionary divergence, our data directly support a theorized conserved element for long distance mechanochemical coupling in kinesin, myosin, and F(1)-ATPase. These findings also suggest that these relatively rapid IR approaches can provide structural biomarkers for clinical determination of drug sensitivity and drug efficacy in nucleotide triphosphatases.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-like protein KIF11	A	369	Homo sapiens	Mutation(s): 0  Gene Names: EG5, KIF11, KNSL1, TRIP5
UniProt & NIH Common Fund Data Resources
Find proteins for P52732 (Homo sapiens) Explore P52732  Go to UniProtKB:  P52732
PHAROS:  P52732

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZZD	C [auth A]	S-TRITYL-L-CYSTEINE C22 H21 N O2 S DLMYFMLKORXJPO-FQEVSTJZSA-N
KEN	D [auth A]	N,N-dimethylmethanamine C3 H9 N GETQZCLCWQTVFV-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ZZD	BindingDB:  3KEN	Ki: min: 50, max: 143.8 (nM) from 6 assay(s)
		IC50: min: 140, max: 1950 (nM) from 9 assay(s)
		EC50: 1720 (nM) from 1 assay(s)
	PDBBind:  3KEN	IC50: 4000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.275 
• R-Value Work: 0.241 
• Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.93	α = 90
b = 157.93	β = 90
c = 157.93	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
SAINT	data reduction
PROTEUM PLUS	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-10-26 
• Released Date: 2010-03-16 
Deposition Author(s): Parke, C.L., Wojcik, E.J., Kim, S., Worthylake, D.K.

Revision History  

• Version 1.0: 2010-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance