2WOG

Intermediate and final states of human kinesin Eg5 in complex with S-trityl-L-cysteine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

An Allosteric Transition Trapped in an Intermediate State of a New Kinesin-Inhibitor Complex.

Kaan, H.Y.K.Ulaganathan, V.Hackney, D.D.Kozielski, F.

(2010) Biochem J 425: 55

  • DOI: 10.1042/BJ20091207
  • Primary Citation of Related Structures:  
    2WOG

  • PubMed Abstract: 
  • Human kinesin Eg5 plays an essential role in mitosis by separating duplicated centrosomes and establishing the bipolar spindle. Eg5 is an interesting drug target for the development of cancer chemotherapy, with seven inhibitors already in clinical tr ...

    Human kinesin Eg5 plays an essential role in mitosis by separating duplicated centrosomes and establishing the bipolar spindle. Eg5 is an interesting drug target for the development of cancer chemotherapy, with seven inhibitors already in clinical trials. In the present paper, we report the crystal structure of the Eg5 motor domain complexed with a potent antimitotic inhibitor STLC (S-trityl-L-cysteine) to 2.0 A (1 A=0.1 nm) resolution. The Eg5-STLC complex crystallizes in space group P3(2) with three molecules per asymmetric unit. Two of the molecules reveal the final inhibitor-bound state of Eg5, whereby loop L5 has swung downwards to close the inhibitor-binding pocket, helix alpha4 has rotated by approx. 15 degrees and the neck-linker has adopted a docked conformation. The third molecule, however, revealed an unprecedented intermediate state, whereby local changes at the inhibitor-binding pocket have not propagated to structural changes at the switch II cluster and neck-linker. This provides structural evidence for the sequence of drug-induced conformational changes.


    Organizational Affiliation

    The Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
KINESIN-LIKE PROTEIN KIF11ABC368Homo sapiensMutation(s): 0 
Gene Names: KIF11EG5KNSL1TRIP5
Find proteins for P52732 (Homo sapiens)
Explore P52732 
Go to UniProtKB:  P52732
NIH Common Fund Data Resources
PHAROS  P52732
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A, B, C
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ZZD
Query on ZZD

Download CCD File 
A, B, C
S-TRITYL-L-CYSTEINE
C22 H21 N O2 S
DLMYFMLKORXJPO-FQEVSTJZSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C
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
ZZDIC50:  620   nM  BindingDB
ZZDKi:  71.9000015258789   nM  BindingDB
ZZDIC50:  1000   nM  BindingDB
ZZDIC50:  185.89999389648438   nM  BindingDB
ZZDIC50:  352   nM  BindingDB
ZZDEC50:  1720   nM  BindingDB
ZZDKi:  50   nM  BindingDB
ZZDKi:  107   nM  BindingDB
ZZDKi:  143.8000030517578   nM  BindingDB
ZZDIC50:  140   nM  BindingDB
ZZDIC50:  1950   nM  BindingDB
ZZDIC50:  1900   nM  BindingDB
ZZDKi:  129   nM  BindingDB
ZZDIC50:  1800   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.158 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.5α = 90
b = 96.5β = 90
c = 124.441γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-15
    Changes: Advisory, Data collection, Experimental preparation, Other