4N9R

X-ray structure of the complex between hen egg white lysozyme and pentacholrocarbonyliridate(III) (1 day)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Interaction between proteins and Ir based CO releasing molecules: mechanism of adduct formation and CO release.

Petruk, A.A.Vergara, A.Marasco, D.Bikiel, D.Doctorovich, F.Estrin, D.A.Merlino, A.

(2014) Inorg.Chem. 53: 10456-10462

  • DOI: 10.1021/ic501498g
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Carbon monoxide releasing molecules (CORMs) have important bactericidal, anti-inflammatory, neuroprotective, and antiapoptotic effects and can be used as tools for CO physiology experiments, including studies on vasodilation. In this context, a new c ...

    Carbon monoxide releasing molecules (CORMs) have important bactericidal, anti-inflammatory, neuroprotective, and antiapoptotic effects and can be used as tools for CO physiology experiments, including studies on vasodilation. In this context, a new class of CO releasing molecules, based on pentachlorocarbonyliridate(III) derivative have been recently reported. Although there is a growing interest in the characterization of protein-CORMs interactions, only limited structural information on CORM binding to protein and CO release has been available to date. Here, we report six different crystal structures describing events ranging from CORM entrance into the protein crystal up to the CO release and a biophysical characterization by isothermal titration calorimetry, Raman microspectroscopy, and molecular dynamics simulations of the complex between a pentachlorocarbonyliridate(III) derivative and hen egg white lysozyme, a model protein. Altogether, the data indicate the formation of a complex in which the ligand can bind to different sites of the protein surface and provide clues on the mechanism of adduct formation and CO release.


    Organizational Affiliation

    Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, University of Buenos Aires , Ciudad Universitaria, Pab. 2, C1428EHA Buenos Aires, Argentina.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
2T8
Query on 2T8

Download SDF File 
Download CCD File 
A
carbonyl(tetrachloro)oxidoiridium
C Cl4 Ir O2
OTOHNVZCVDSLDT-UHFFFAOYSA-J
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.319α = 90.00
b = 78.319β = 90.00
c = 37.049γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSphasing
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-30
    Type: Initial release