8OM8

X-ray structure of lysozyme obtained upon reaction with [VIVO(empp)2] (Structure A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.148 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Implications of Protein Interaction in the Speciation of Potential V IV O-Pyridinone Drugs.

Ferraro, G.Paolillo, M.Sciortino, G.Pisanu, F.Garribba, E.Merlino, A.

(2023) Inorg Chem 62: 8407-8417

  • DOI: https://doi.org/10.1021/acs.inorgchem.3c01041
  • Primary Citation of Related Structures:  
    8OM8, 8OMS, 8OMT

  • PubMed Abstract: 

    Vanadium complexes (VCs) are promising agents for the treatment, among others, of diabetes and cancer. The development of vanadium-based drugs is mainly limited by a scarce knowledge of the active species in the target organs, which is often determined by the interaction of VCs with biological macromolecules like proteins. Here, we have studied the binding of [V IV O(empp) 2 ] (where Hempp is 1-methyl-2-ethyl-3-hydroxy-4(1 H )-pyridinone), an antidiabetic and anticancer VC, with the model protein hen egg white lysozyme (HEWL) by electrospray ionization-mass spectrometry (ESI-MS), electron paramagnetic resonance (EPR), and X-ray crystallography. ESI-MS and EPR techniques reveal that, in aqueous solution, both the species [V IV O(empp) 2 ] and [V IV O(empp)(H 2 O)] + , derived from the first one upon the loss of a empp(-) ligand, interact with HEWL. Crystallographic data, collected under different experimental conditions, show covalent binding of [V IV O(empp)(H 2 O)] + to the side chain of Asp48, and noncovalent binding of cis -[V IV O(empp) 2 (H 2 O)], [V IV O(empp)(H 2 O)] + , [V IV O(empp)(H 2 O) 2 ] + , and of an unusual trinuclear oxidovanadium(V) complex, [V V 3 O 6 (empp) 3 (H 2 O)], with accessible sites on the protein surface. The possibility of covalent and noncovalent binding with different strength and of interaction with various sites favor the formation of adducts with the multiple binding of vanadium moieties, allowing the transport in blood and cellular fluids of more than one metal-containing species with a possible amplification of the biological effects.


  • 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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VSU (Subject of Investigation/LOI)
Query on VSU

Download Ideal Coordinates CCD File 
C [auth AAA]tris-[(1-methyl-2-ethyl-3-hydroxy-4(1H)-pyridinone)]-V(V)3O7
C24 H30 N3 O13 V3
LBUGGDQMXYMIIZ-UHFFFAOYSA-K
VTZ
Query on VTZ

Download Ideal Coordinates CCD File 
D [auth AAA]1-methyl-2-ethyl-3-hydroxy-4(1H)-pyridinone)V(IV)O4
C8 H10 N O6 V
PNFKDCNTOXLWCD-UHFFFAOYSA-M
ACT
Query on ACT

Download Ideal Coordinates CCD File 
B [auth AAA]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth AAA],
F [auth AAA],
G [auth AAA],
H [auth AAA]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.148 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.06α = 90
b = 78.06β = 90
c = 37.01γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary