8D52

Parathyroid hormone 1 receptor extracellular domain complexed with a peptide ligand containing (2-naphthyl)-beta-3-homoalanine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Harnessing Aromatic-Histidine Interactions through Synergistic Backbone Extension and Side Chain Modification.

Yu, Z.Kreitler, D.F.Chiu, Y.T.T.Xu, R.Bruchs, A.T.Bingman, C.A.Gellman, S.H.

(2023) Angew Chem Int Ed Engl 62: e202308100-e202308100

  • DOI: https://doi.org/10.1002/anie.202308100
  • Primary Citation of Related Structures:  
    8D51, 8D52

  • PubMed Abstract: 

    Peptide engineering efforts have delivered drugs for diverse human diseases. Side chain alteration is among the most common approaches to designing new peptides for specific applications. The peptide backbone can be modified as well, but this strategy has received relatively little attention. Here we show that new and favorable contacts between a His side chain on a target protein and an aromatic side chain on a synthetic peptide ligand can be engineered by rational and coordinated side chain modification and backbone extension. Side chain modification alone was unsuccessful. Binding measurements, high-resolution structural studies and pharmacological outcomes all support the synergy between backbone and side chain modification in engineered ligands of the parathyroid hormone receptor-1, which is targeted by osteoporosis drugs. These results should motivate other structure-based designs featuring coordinated side chain modification and backbone extension to enhance the engagement of peptide ligands with target proteins.


  • Organizational Affiliation

    Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Parathyroid hormone/parathyroid hormone-related peptide receptor103Homo sapiensMutation(s): 0 
Gene Names: PTH1RPTHRPTHR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q03431 (Homo sapiens)
Explore Q03431 
Go to UniProtKB:  Q03431
PHAROS:  Q03431
GTEx:  ENSG00000160801 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03431
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PTHrP[1-36]22Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P12272 (Homo sapiens)
Explore P12272 
Go to UniProtKB:  P12272
PHAROS:  P12272
GTEx:  ENSG00000087494 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12272
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.383α = 90
b = 57.383β = 90
c = 205.208γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata processing
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM056414

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2023-12-27
    Changes: Database references