5JVX

X-ray structure of the adduct formed in the reaction between thaumatin and a gold carbene compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.187 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 6O0Click on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

First Crystal Structure for a Gold Carbene-Protein Adduct.

Ferraro, G.Gabbiani, C.Merlino, A.

(2016) Bioconjug Chem 27: 1584-1587

  • DOI: https://doi.org/10.1021/acs.bioconjchem.6b00298
  • Primary Citation of Related Structures:  
    5JVX

  • PubMed Abstract: 

    The X-ray structure of the adduct formed in the reaction between the gold N-heterocyclic carbene compound Au(NHC)Cl (with NHC = 1-butyl-3-methyl-imidazole-2-ylidene) and the model protein thaumatin is reported here. The structure reveals binding of Au(NHC)(+) fragments to distinct protein sites. Notably, binding of the gold compound occurs at lysine side chains and at the N-terminal tail; the metal binds the protein after releasing Cl(-) ligand, but retaining NHC fragment.


  • Organizational Affiliation

    Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo , Via Cintia, I-80126 Napoli, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thaumatin-1207Thaumatococcus danielliiMutation(s): 0 
UniProt
Find proteins for P02883 (Thaumatococcus daniellii)
Explore P02883 
Go to UniProtKB:  P02883
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02883
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6O0
Query on 6O0

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
(1-butyl-3-methyl-1,3-dihydro-2H-imidazol-2-ylidene)(chloro)gold
C8 H14 Au Cl N2
VPJMTYLCIKLAAU-UHFFFAOYSA-M
TLA
Query on TLA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.187 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.912α = 90
b = 57.912β = 90
c = 150.136γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 6O0Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2016-07-27
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary