Quasi-racemic structure of [G6A]kalata B1

Experimental Data Snapshot

  • Resolution: 1.25 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

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This is version 1.3 of the entry. See complete history


Racemic and Quasi-Racemic X-ray Structures of Cyclic Disulfide-Rich Peptide Drug Scaffolds.

Wang, C.K.King, G.J.Northfield, S.E.Ojeda, P.G.Craik, D.J.

(2014) Angew Chem Int Ed Engl 53: 11236-11241

  • DOI: https://doi.org/10.1002/anie.201406563
  • Primary Citation of Related Structures:  
    4TTK, 4TTL, 4TTM, 4TTN, 4TTO

  • PubMed Abstract: 

    Cyclic disulfide-rich peptides have exceptional stability and are promising frameworks for drug design. We were interested in obtaining X-ray structures of these peptides to assist in drug design applications, but disulfide-rich peptides can be notoriously difficult to crystallize. To overcome this limitation, we chemically synthesized the L- and D-forms of three prototypic cyclic disulfide-rich peptides: SFTI-1 (14-mer with one disulfide bond), cVc1.1 (22-mer with two disulfide bonds), and kB1 (29-mer with three disulfide bonds) for racemic crystallization studies. Facile crystal formation occurred from a racemic mixture of each peptide, giving structures solved at resolutions from 1.25 Å to 1.9 Å. Additionally, we obtained the quasi-racemic structures of two mutants of kB1, [G6A]kB1, and [V25A]kB1, which were solved at a resolution of 1.25 Å and 2.3 Å, respectively. The racemic crystallography approach appears to have broad utility in the structural biology of cyclic peptides.

  • Organizational Affiliation

    Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, 4072 (Australia).

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kalata-B129Oldenlandia affinisMutation(s): 1 
Find proteins for P56254 (Oldenlandia affinis)
Explore P56254 
Go to UniProtKB:  P56254
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56254
Sequence Annotations
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
D-kalata B129synthetic constructMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MPD

Download Ideal Coordinates CCD File 
C6 H14 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.25 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P -1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 22.186α = 93.8
b = 25.923β = 106.59
c = 37.713γ = 99.91
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-10-22
    Changes: Database references
  • Version 1.2: 2015-02-04
    Changes: Derived calculations
  • Version 1.3: 2023-12-27
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy