5K86 | pdb_00005k86

Aza-glycine containing collagen peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 
    0.159 (Depositor), 0.160 (DCC) 
  • R-Value Work: 
    0.129 (Depositor), 0.129 (DCC) 
  • R-Value Observed: 
    0.132 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.0 of the entry. See complete history

Literature

Structural Basis for Aza-Glycine Stabilization of Collagen.

Kasznel, A.J.Zhang, Y.Hai, Y.Chenoweth, D.M.

(2017) J Am Chem Soc 139: 9427-9430

  • DOI: https://doi.org/10.1021/jacs.7b03398
  • Primary Citation Related Structures: 
    5K86

  • PubMed Abstract: 

    Previously, we have demonstrated that replacement of the strictly conserved glycine in collagen with aza-glycine provides a general solution for stabilizing triple helical collagen peptides (Chenoweth, D. M.; et al. J. Am. Chem. Soc. 2016, 138, 9751 ; 2015, 137, 12422 ). The additional hydrogen bond and conformational constraints provided by aza-glycine increases the thermal stability and rate of folding in collagen peptides composed of Pro-Hyp-Gly triplet repeats, allowing for truncation to the smallest self-assembling peptide systems observed to date. Here we show that aza-glycine substitution enhances the stability of an arginine-containing collagen peptide and provide a structural basis for this stabilization with an atomic resolution crystal structure. These results demonstrate that a single nitrogen atom substitution for a glycine alpha-carbon increases the peptide's triple helix melting temperature by 8.6 °C. Furthermore, we provide the first structural basis for stabilization of triple helical collagen peptides containing aza-glycine and we demonstrate that minimal alteration to the peptide backbone conformation occurs with aza-glycine incorporation.


  • Organizational Affiliation
    • Department of Chemistry and ‡Department of Bioengineering, University of Pennsylvania , Philadelphia, Pennsylvania 19104-6323, United States.

Macromolecule Content 

  • Total Structure Weight: 6.69 kDa 
  • Atom Count: 607 
  • Modeled Residue Count: 75 
  • Deposited Residue Count: 75 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Aza-glycine containing collagen peptide
A, B, C
25synthetic constructMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HYP
Query on HYP
A, B, C
L-PEPTIDE LINKINGC5 H9 N O3PRO
XZA
Query on XZA
A, B, C
PEPTIDE-LIKEC H4 N2 O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free:  0.159 (Depositor), 0.160 (DCC) 
  • R-Value Work:  0.129 (Depositor), 0.129 (DCC) 
  • R-Value Observed: 0.132 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.49α = 90
b = 18.24β = 91.66
c = 48.84γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
University of PennsylvaniaUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-12
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection