4R6G

Crystal structure of computational designed leucine rich repeats DLRR_K in space group P22121


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Control of repeat-protein curvature by computational protein design.

Park, K.Shen, B.W.Parmeggiani, F.Huang, P.S.Stoddard, B.L.Baker, D.

(2015) Nat.Struct.Mol.Biol. 22: 167-174

  • DOI: 10.1038/nsmb.2938
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Shape complementarity is an important component of molecular recognition, and the ability to precisely adjust the shape of a binding scaffold to match a target of interest would greatly facilitate the creation of high-affinity protein reagents and th ...

    Shape complementarity is an important component of molecular recognition, and the ability to precisely adjust the shape of a binding scaffold to match a target of interest would greatly facilitate the creation of high-affinity protein reagents and therapeutics. Here we describe a general approach to control the shape of the binding surface on repeat-protein scaffolds and apply it to leucine-rich-repeat proteins. First, self-compatible building-block modules are designed that, when polymerized, generate surfaces with unique but constant curvatures. Second, a set of junction modules that connect the different building blocks are designed. Finally, new proteins with custom-designed shapes are generated by appropriately combining building-block and junction modules. Crystal structures of the designs illustrate the power of the approach in controlling repeat-protein curvature.


    Organizational Affiliation

    1] Department of Biochemistry, University of Washington, Seattle, Washington, USA. [2] Institute for Protein Design, University of Washington, Seattle, Washington, USA. [3] Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA.,Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,1] Department of Biochemistry, University of Washington, Seattle, Washington, USA. [2] Institute for Protein Design, University of Washington, Seattle, Washington, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
leucine rich repeats DLRR_K
A
464N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.208 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.868α = 90.00
b = 93.369β = 90.00
c = 126.237γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CrystalCleardata collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-07
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Database references
  • Version 1.2: 2015-01-28
    Type: Database references
  • Version 1.3: 2015-02-18
    Type: Database references