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

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.241 

Starting Model: experimental
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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

  • DOI: https://doi.org/10.1074/jbc.M109.092072
  • Primary Citation of Related Structures:  

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-like protein KIF11369Homo sapiensMutation(s): 0 
Gene Names: EG5KIF11KNSL1TRIP5
UniProt & NIH Common Fund Data Resources
Find proteins for P52732 (Homo sapiens)
Explore P52732 
Go to UniProtKB:  P52732
GTEx:  ENSG00000138160 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52732
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding 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

  • 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 = 157.93α = 90
b = 157.93β = 90
c = 157.93γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
SAINTdata reduction
PROTEUM PLUSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description