Structure of Pin1 WW Domain Variant 1 with beta3-Ser Loop Substitution

Experimental Data Snapshot

  • Resolution: 1.99 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report

This is version 2.0 of the entry. See complete history


Evaluation of beta-Amino Acid Replacements in Protein Loops: Effects on Conformational Stability and Structure.

Mortenson, D.E.Kreitler, D.F.Thomas, N.C.Guzei, I.A.Gellman, S.H.Forest, K.T.

(2018) Chembiochem 19: 604-612

  • DOI: https://doi.org/10.1002/cbic.201700580
  • Primary Citation of Related Structures:  
    5VTI, 5VTJ, 5VTK

  • PubMed Abstract: 

    β-Amino acids have a backbone that is expanded by one carbon atom relative to α-amino acids, and β residues have been investigated as subunits in protein-like molecules that adopt discrete and predictable conformations. Two classes of β residue have been widely explored in the context of generating α-helix-like conformations: β 3 -amino acids, which are homologous to α-amino acids and bear a side chain on the backbone carbon adjacent to nitrogen, and residues constrained by a five-membered ring, such the one derived from trans-2-aminocyclopentanecarboxylic acid (ACPC). Substitution of α residues with their β 3  homologues within an α-helix-forming sequence generally causes a decrease in conformational stability. Use of a ring-constrained β residue, however, can offset the destabilizing effect of α→β substitution. Here we extend the study of α→β substitutions, involving both β 3 and ACPC residues, to short loops within a small tertiary motif. We start from previously reported variants of the Pin1 WW domain that contain a two-, three-, or four-residue β-hairpin loop, and we evaluate α→β replacements at each loop position for each variant. By referral to the ϕ,ψ angles of the native structure, one can choose a stereochemically appropriate ACPC residue. Use of such logically chosen ACPC residues enhances conformational stability in several cases. Crystal structures of three β-containing Pin1 WW domain variants show that a native-like tertiary structure is maintained in each case.

  • Organizational Affiliation

    Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 134Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13526 (Homo sapiens)
Explore Q13526 
Go to UniProtKB:  Q13526
PHAROS:  Q13526
GTEx:  ENSG00000127445 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13526
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.99 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.163 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.629α = 90
b = 47.629β = 90
c = 60.741γ = 120
Software Package:
Software NamePurpose
XPREPdata reduction
APEX 2data collection
XPREPdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection