3KEN

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

Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


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

  • 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 ...

    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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kinesin-like protein KIF11A369Homo sapiensMutation(s): 0 
Gene Names: EG5, KIF11, KNSL1, TRIP5
Find proteins for P52732 (Homo sapiens)
Explore P52732 
Go to UniProtKB:  P52732
NIH Common Fund Data Resources
PHAROS:  P52732
GTEx:  ENSG00000138160
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download Ideal Coordinates CCD File 
 B [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
ZZD
Query on ZZD
Download Ideal Coordinates CCD File 
 C [auth A]S-TRITYL-L-CYSTEINE
C22 H21 N O2 S
DLMYFMLKORXJPO-FQEVSTJZSA-N		 Ligand Interaction
KEN
Query on KEN
Download Ideal Coordinates CCD File 
 D [auth A]N,N-dimethylmethanamine
C3 H9 N
GETQZCLCWQTVFV-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
 E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZZDKi:  135.89999389648438   nM  BindingDB
ZZDIC50:  284.8999938964844   nM  BindingDB
ZZDKi:  50   nM  BindingDB
ZZDIC50:  1950   nM  BindingDB
ZZDKi:  71.9000015258789   nM  BindingDB
ZZDIC50:  1900   nM  BindingDB
ZZDEC50:  1720   nM  BindingDB
ZZDIC50 :  4000   nM  PDBBind
ZZDIC50:  620   nM  BindingDB
ZZDIC50:  140   nM  BindingDB
ZZDKi:  129   nM  BindingDB
ZZDIC50:  352   nM  BindingDB
ZZDIC50:  1800   nM  BindingDB
ZZDIC50:  1000   nM  BindingDB
ZZDKi:  107   nM  BindingDB
ZZDKi:  143.8000030517578   nM  BindingDB
ZZDIC50:  185.89999389648438   nM  BindingDB
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 = 157.93α = 90
b = 157.93β = 90
c = 157.93γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
SAINTdata reduction
PROTEUM PLUSdata scaling
AMoREphasing

Structure Validation

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View more in-depth experimental data

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