5NN2

The structure of the polo-box domain (PBD) of Plk1 in complex with Z228588490

• PDB DOI: https://doi.org/10.2210/pdb5NN2/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-04-07 Released: 2018-02-21 
• Deposition Author(s): Kunciw, D.L., Rossmann, M., Stokes, J.E., De Fusco, C., Spring, D.R., Hyvonen, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.219 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

A fragment-based approach to developing inhibitors of the cryptic pocket of the Polo-Like Kinase 1 Polo-Box Domain.

Kunciw, D.L., De Fusco, C., Rossmann, M., Stokes, J.E., Renzetti, A., Sore, H.F., Hyvonen, M., Spring, D.R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 27 kDa 
• Atom Count: 1,830 
• Modelled Residue Count: 218 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PLK1	A	232	Homo sapiens	Mutation(s): 0  Gene Names: PLK1, PLK EC: 2.7.11.21
UniProt & NIH Common Fund Data Resources
Find proteins for P53350 (Homo sapiens) Explore P53350  Go to UniProtKB:  P53350
PHAROS:  P53350 GTEx:  ENSG00000166851

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Z24	B [auth A]	(3~{R},5~{R})-1-[2,4-bis(fluoranyl)phenyl]-5-oxidanyl-pyrrolidine-3-carboxylic acid C11 H11 F2 N O3 HKKAZODAIOIPGM-LHLIQPBNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.219 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.36	α = 90
b = 93.38	β = 100.72
c = 35.9	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-21 
Deposition Author(s): Kunciw, D.L., Rossmann, M., Stokes, J.E., De Fusco, C., Spring, D.R., Hyvonen, M.

Revision History  

• Version 1.0: 2018-02-21
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Data collection, Database references