8PTE

Polyoxidovanadate interaction with proteins: crystal structure of lysozyme bound to octadecavanadate ion (structure B)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.180 

wwPDB Validation   3D Report Full Report


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Literature

Stabilization and Binding of [V 4 O 12 ] 4- and Unprecedented [V 20 O 54 (NO 3 )] n- to Lysozyme upon Loss of Ligands and Oxidation of the Potential Drug V IV O(acetylacetonato) 2.

Ferraro, G.Tito, G.Sciortino, G.Garribba, E.Merlino, A.

(2023) Angew Chem Int Ed Engl 62: e202310655-e202310655

  • DOI: https://doi.org/10.1002/anie.202310655
  • Primary Citation of Related Structures:  
    7ZU6, 8PTE

  • PubMed Abstract: 

    High-resolution crystal structures of lysozyme in the presence of the potential drug V IV O(acetylacetonato) 2 under two different experimental conditions have been solved. The crystallographic study reveals the loss of the ligands, the oxidation of V IV to V V and the subsequent formation of adducts of the protein with two different polyoxidovanadates: [V 4 O 12 ] 4- , which interacts with lysozyme non-covalently, and the unprecedented [V 20 O 54 (NO 3 )] n- , which is covalenty bound to the side chain of an aspartate residue of symmetry related molecules.


  • 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
Lysozyme CA [auth AAA]129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JQJ (Subject of Investigation/LOI)
Query on JQJ

Download Ideal Coordinates CCD File 
C [auth AAA]Polyoxidovanadate complex
O54 V20
YKPFHFIARSLXOW-UHFFFAOYSA-A
H1W (Subject of Investigation/LOI)
Query on H1W

Download Ideal Coordinates CCD File 
D [auth AAA]pentakis(oxidanyl)vanadium
H5 O5 V
QKDGGEBMABOMMW-UHFFFAOYSA-I
NO3
Query on NO3

Download Ideal Coordinates CCD File 
E [auth AAA],
F [auth AAA],
G [auth AAA]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth AAA]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.180 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.39α = 90
b = 80.39β = 90
c = 36.51γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-10
    Type: Initial release