9GOG | pdb_00009gog

X-ray structure of lysozyme obtained upon reaction with the dioxidovanadium(V) complex with furan-2-carboxylic acid (3-ethoxy-2-hydroxybenzylidene)hydrazide

  • Classification: HYDROLASE
  • Organism(s): Gallus gallus
  • Mutation(s): No 

  • Deposited: 2024-09-05 Released: 2024-12-18 
  • Deposition Author(s): Paolillo, M., Ferraro, G., Merlino, A.
  • Funding Organization(s): Ministero dell Universita e della Ricerca, Council of Scientific & Industrial Research (CSIR), Science and Engineering Research Board (SERB)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 
    0.256 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.213 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Interaction of V V O 2 -hydrazonates with lysozyme.

Paolillo, M.Ferraro, G.Sahu, G.Pattanayak, P.D.Garribba, E.Halder, S.Ghosh, R.Mondal, B.Chatterjee, P.B.Dinda, R.Merlino, A.

(2024) J Inorg Biochem 264: 112787-112787

  • DOI: https://doi.org/10.1016/j.jinorgbio.2024.112787
  • Primary Citation of Related Structures:  
    9GOG, 9GOK

  • PubMed Abstract: 

    Vanadium compounds (VCs) exhibit a broad range of pharmacological properties, with their most significant medical applications being in the treatment of cancer and diabetes. The therapeutic effects and mode of action of VCs may be associated with their ability to bind proteins and, consequently, understanding the VC-protein interaction is of paramount importance. Among the promising VCs, the V V O 2 complex with the aroylhydrazone furan-2-carboxylic acid ((3-ethoxy-2-hydroxybenzylidene)hydrazide, hereafter denoted as VC1), deserves attention, since it exhibits cytotoxicity against various cancer cell lines, including HeLa. The interaction between VC1 and its analogue, denoted as VC2 (the dioxidovanadium(V) complex with (E)-N'-(1-(2-hydroxy-5-methoxyphenyl)ethylidene)furan-2-carbohydrazide), and hen egg white lysozyme (HEWL) was examined by UV-vis spectroscopy, fluorescence, circular dichroism, and X-ray crystallography. The interaction of VC1 and VC2 with HEWL does not alter the protein secondary and tertiary structure. Crystallographic studies indicate that the two metal complexes or V-containing fragments originating from VC1 and VC2 bind the protein via non-covalent interactions. Furthermore, when bound to HEWL, two VC1 molecules and two VC2 molecules form a supramolecular association stabilized by stacking interactions. This type of interaction could favour the binding of similar compounds to proteins and affect their biological activity.


  • 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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IOM
Query on A1IOM

Download Ideal Coordinates CCD File 
G [auth AAA],
H [auth AAA]
dioxidovanadium(V) complex with furan-2-carboxylic acid (3-ethoxy-2-hydroxybenzylidene)hydrazide
C14 H12 N2 O6 V
CYYWESREVLZULB-SFRYUHGMSA-L
VVB (Subject of Investigation/LOI)
Query on VVB

Download Ideal Coordinates CCD File 
F [auth AAA]bis(oxidanyl)vanadium
H2 O2 V
UVEFAEMXFFXFKB-UHFFFAOYSA-L
ACT
Query on ACT

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D [auth AAA],
E [auth AAA]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth AAA]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free:  0.256 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.213 (DCC) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.846α = 90
b = 76.846β = 90
c = 36.839γ = 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
Ministero dell Universita e della RicercaItaly2022JMFC3X
Council of Scientific & Industrial Research (CSIR)India01(3073)/21/EMR-II
Science and Engineering Research Board (SERB)IndiaCRG/2023/000884

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-18
    Type: Initial release