2V5Q

CRYSTAL STRUCTURE OF WILD-TYPE PLK-1 KINASE DOMAIN IN COMPLEX WITH A SELECTIVE DARPIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure Pf Wild-Type Plk-1 Kinase Domain in Complex with a Selective Darpin

Bandeiras, T.M.Hillig, R.C.Matias, P.M.Eberspaecher, U.Fanghaenel, J.Thomaz, M.Miranda, S.Crusius, K.Puetter, V.Amstutz, P.Gulotti-Georgieva, M.Binz, H.K.Holz, C.Schmitz, A.A.P.Lang, C.Donner, P.Egner, U.Carrondo, M.A.Mueller-Tiemann, B.

(2008) Acta Crystallogr.,Sect.D 64: 339

  • DOI: 10.1107/S0907444907068217

  • PubMed Abstract: 
  • As a key regulator of mitosis, the Ser/Thr protein polo-like kinase-1 (Plk-1) is a well validated drug target in cancer therapy. In order to enable structure-guided drug design, determination of the crystal structure of the kinase domain of Plk-1 was ...

    As a key regulator of mitosis, the Ser/Thr protein polo-like kinase-1 (Plk-1) is a well validated drug target in cancer therapy. In order to enable structure-guided drug design, determination of the crystal structure of the kinase domain of Plk-1 was attempted. Using a multi-parallel cloning and expression approach, a set of length variants were identified which could be expressed in large amounts from insect cells and which could be purified to high purity. However, all attempts to crystallize these constructs failed. Crystals were ultimately obtained by generating designed ankyrin-repeat proteins (DARPins) selective for Plk-1 and using them for cocrystallization. Here, the first crystal structure of the kinase domain of wild-type apo Plk-1, in complex with DARPin 3H10, is presented, underlining the power of selective DARPins as crystallization tools. The structure was refined to 2.3 A resolution and shows the active conformation of Plk-1. It broadens the basis for modelling and cocrystallization studies for drug design. The binding epitope of 3H10 is rich in arginine, glutamine and lysine residues, suggesting that the DARPin enabled crystallization by masking a surface patch which is unfavourable for crystal contact formation. Based on the packing observed in the crystal, a truncated DARPin variant was designed which showed improved binding characteristics.


    Organizational Affiliation

    Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780 Oeiras, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERINE/THREONINE-PROTEIN KINASE PLK1
A, B
315Homo sapiensMutation(s): 0 
Gene Names: PLK1 (PLK)
EC: 2.7.11.21
Find proteins for P53350 (Homo sapiens)
Go to Gene View: PLK1
Go to UniProtKB:  P53350
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DESIGN ANKYRIN REPEAT PROTEIN
C, D
167N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.329α = 90.00
b = 135.225β = 90.00
c = 136.824γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance