Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 28.15 kDa 
• Atom Count: 2,141 
• Modelled Residue Count: 226 
• Deposited Residue Count: 244 
• Unique protein chains: 2

 4DFW

Oxime-based Post Solid-phase Peptide Diversification: Identification of High Affinity Polo-like Kinase 1 (Plk1) Polo-box Domain Binding Peptides

• PDB DOI:  https://doi.org/10.2210/pdb4DFW/pdb

• Classification: TRANSCRIPTION/Antagonist
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-24 Released: 2012-03-28 
• Deposition Author(s): Liu, F., Park, J.-E., Qian, W.-J., Lim, D., Gr ber, M., Berg, T., Yaffe, M.B., Lee, K.S., Burke Jr., T.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.196 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 

Literature

Oxime-based Post Solid-phase Peptide Diversification: Identification of High Affinity Polo-like Kinase 1 (Plk1) Polo-box Domain Binding Peptides

Liu, F., Park, J.-E., Qian, W.-J., Lim, D., Scharow, A., Berg, T., Yaffe, M.B., Lee, K.S., Burke, T.R.

(2012) Chem Biol 

• PubMed: 22292814 
• DOI: https://doi.org/10.1021/cb200469a
• Primary Citation of Related Structures:  
  4DFW


• PubMed Abstract: 
  

In an effort to develop improved binding antagonists of the polo-like kinase 1 (Plk1) polo-box domain (PBD), we optimized interactions of the known high affinity 5-mer peptide PLHSpT using oxime-based post solid-phase peptide diversification of the N-terminal Pro residue. This allowed us to achieve up to two orders of magnitude potency enhancement. An X-ray crystal structure of the highest affinity analogue in complex with Plk1 PBD revealed new binding interactions in a hydrophobic channel that had been occluded in X-ray structures of the unliganded protein. This study represents an important example where amino acid modification by post solid-phase oxime ligation can facilitate the development of protein-protein interaction inhibitors by identifying new binding pockets that would not otherwise be accessible to coded amino acid residues.

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Organizational Affiliation: 

Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PLK1	A	237	Homo sapiens	Mutation(s): 0  Gene Names: PLK, PLK1 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide	B [auth D]	7	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
0LF	B [auth D]	L-PEPTIDE LINKING	C15 H21 N O3		PRO
TPO	B [auth D]	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.196 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.665	α = 76.44
b = 34.844	β = 86.95
c = 47.097	γ = 69.14

Software Package:

Software Name	Purpose
StructureStudio	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-28 
Deposition Author(s): Liu, F., Park, J.-E., Qian, W.-J., Lim, D., Gr ber, M., Berg, T., Yaffe, M.B., Lee, K.S., Burke Jr., T.R.

Revision History  

• Version 1.0: 2012-03-28
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Structure summary