Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 107.62 kDa 
• Atom Count: 6929 
• Residue Count: 829 
• Unique protein chains: 2

2V5Q

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

• DOI: 10.2210/pdb2V5Q/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2007-07-08 Released: 2008-04-01 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.224 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Structure of wild-type Plk-1 kinase domain in complex with a selective DARPin.

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

(2008) Acta Crystallogr D Biol Crystallogr 64: 339-353

• PubMed: 18391401 
• DOI: 10.1107/S0907444907068217
• Primary Citation of Related Structures:  
  2V5Q


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE PLK1	A, B	315	Homo sapiens	Mutation(s): 0  Gene Names: PLK1, PLK EC: 2.7.11.21
Find proteins for P53350 (Homo sapiens) Explore P53350  Go to UniProtKB:  P53350
NIH Common Fund Data Resources
PHAROS:  P53350 GTEx:  ENSG00000166851

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DESIGN ANKYRIN REPEAT PROTEIN	C, D	167	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.224 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.329	α = 90
b = 135.225	β = 90
c = 136.824	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-07-08 
• Released Date: 2008-04-01 
Deposition Author(s): 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.

Revision History 

• Version 1.0: 2008-04-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2019-02-20
  Changes: Data collection, Database references, Experimental preparation, Other, Source and taxonomy