5WBB

Peroxide Activation Regulated by Hydrogen Bonds within Artificial Cu Proteins - S112A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Peroxide Activation Regulated by Hydrogen Bonds within Artificial Cu Proteins.

Mann, S.I.Heinisch, T.Ward, T.R.Borovik, A.S.

(2017) J Am Chem Soc 139: 17289-17292

  • DOI: https://doi.org/10.1021/jacs.7b10452
  • Primary Citation of Related Structures:  
    5WBA, 5WBB, 5WBD, 6ANX

  • PubMed Abstract: 

    Copper-hydroperoxido species (Cu II -OOH) have been proposed to be key intermediates in biological and synthetic oxidations. Using biotin-streptavidin (Sav) technology, artificial copper proteins have been developed to stabilize a Cu II -OOH complex in solution and in crystallo. Stability is achieved because the Sav host provides a local environment around the Cu-OOH that includes a network of hydrogen bonds to the hydroperoxido ligand. Systematic deletions of individual hydrogen bonds to the Cu-OOH complex were accomplished using different Sav variants and demonstrated that stability is achieved with a single hydrogen bond to the proximal O-atom of the hydroperoxido ligand: changing this interaction to only include the distal O-atom produced a reactive variant that oxidized an external substrate.


  • Organizational Affiliation

    Department of Chemistry, University of California , 1102 Natural Science II, Irvine, California 92697, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Streptavidin159Streptomyces avidiniiMutation(s): 1 
UniProt
Find proteins for P22629 (Streptomyces avidinii)
Explore P22629 
Go to UniProtKB:  P22629
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22629
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SQ1
Query on SQ1

Download Ideal Coordinates CCD File 
B [auth A][N-(2-{bis[2-(pyridin-2-yl-kappaN)ethyl]amino-kappaN}ethyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide]copper
C26 H36 Cu N6 O2 S
SAHQKCHSOKYSAG-LTWAPREQSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
C [auth A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.64α = 90
b = 57.64β = 90
c = 183.98γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2017-12-13
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description