4X9R

PLK-1 polo-box domain in complex with Bioactive Imidazolium-containing phosphopeptide macrocycle 3B

• PDB DOI: https://doi.org/10.2210/pdb4X9R/pdb

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


• Deposited: 2014-12-11 Released: 2015-07-29 
• Deposition Author(s): Grant, R.A., Qian, W.-J., Yaffe, M.B., Burke, T.R.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.179 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 

Starting Model: experimental

Literature

Neighbor-directed histidine N ( tau )-alkylation: A route to imidazolium-containing phosphopeptide macrocycles.

Qian, W.J., Park, J.E., Grant, R., Lai, C.C., Kelley, J.A., Yaffe, M.B., Lee, K.S., Burke, T.R.

(2015) Biopolymers 104: 663-673

• PubMed: 26152807 
• DOI: https://doi.org/10.1002/bip.22698
• Primary Citation of Related Structures:  
  4X9R, 4X9V, 4X9W


• PubMed Abstract: 
  

  Our recently discovered, selective, on-resin route to N(τ)-alkylated imidazolium-containing histidine residues affords new strategies for peptide mimetic design. In this, we demonstrate the use of this chemistry to prepare a series of macrocyclic phosphopeptides, in which imidazolium groups serve as ring-forming junctions. Interestingly, these cationic moieties subsequently serve to charge-mask the phosphoamino acid group that directed their formation. Neighbor-directed histidine N(τ)-alkylation opens the door to new families of phosphopeptidomimetics for use in a range of chemical biology contexts.

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Organizational Affiliation: 

Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD, 21702.

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: 28.25 kDa 
• Atom Count: 2,114 
• Modelled Residue Count: 226 
• Deposited Residue Count: 243 
• Unique protein chains: 2

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: 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopeptide macrocycle 3B	B	6	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4L0	B	L-PEPTIDE LINKING	C13 H23 N O4		PRO
56A	B	L-PEPTIDE LINKING	C20 H29 N3 O2		HIS
TPO	B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.179 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.813	α = 90
b = 50.979	β = 100.24
c = 57.59	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-07-29 
Deposition Author(s): Grant, R.A., Qian, W.-J., Yaffe, M.B., Burke, T.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	ES015339
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM68762
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM103403
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357

Revision History  

• Version 1.0: 2015-07-29
  Type: Initial release
  
• Version 1.1: 2016-01-27
  Changes: Database references, Source and taxonomy
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection