4X9R

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


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
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wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PLK1237Homo sapiensMutation(s): 0 
Gene Names: PLK1PLK
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53350
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphopeptide macrocycle 3B6synthetic constructMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
4L0
Query on 4L0
B
L-PEPTIDE LINKINGC13 H23 N O4PRO
56A
Query on 56A
B
L-PEPTIDE LINKINGC20 H29 N3 O2HIS
TPO
Query on TPO
B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
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 = 37.813α = 90
b = 50.979β = 100.24
c = 57.59γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesES015339
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM68762
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103403
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History  (Full details and data files)

  • 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