9RZR | pdb_00009rzr

Hen Egg-White Lysozyme (HEWL) complexed with a Lindqvist-type hexavanadate (V6-Hex) polyoxometalate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 
    0.163 (Depositor), 0.175 (DCC) 
  • R-Value Work: 
    0.140 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 
    0.141 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Finding the Key: Binding of Metal-Oxo Clusters to the Enzyme Active Site Enabled by "Click" (Bio)Conjugation.

Kalandia, G.Declerck, K.Salazar Marcano, D.E.Gourmand, R.Moussawi, M.A.Parac-Vogt, T.N.

(2025) Angew Chem Int Ed Engl 64: e202518349-e202518349

  • DOI: https://doi.org/10.1002/anie.202518349
  • Primary Citation of Related Structures:  
    9RZR, 9RZS, 9RZT

  • PubMed Abstract: 

    Molecular metal-oxo nanoclusters with tunable redox and structural properties have emerged as powerful bio-inorganic tools in catalysis, protein crystallization, and therapeutic applications. Despite their potential, interactions between discrete clusters and proteins are predominantly driven by nonspecific intermolecular interactions, which limit precise control over binding sites and functional outcomes. In this work, we introduce a new strategy to achieve site-directed binding of vanadium-based polyoxometalate clusters (POVs) to distinct regions of Hen Egg White Lysozyme (HEWL), an archetypal antimicrobial enzyme. Three novel hybrid POVs were designed and fully characterized, starting from an azide-functionalized cluster (Na-V 6 -N 3 ), which was subsequently post-functionalized with a hydrophobic hexyne group (Na-V 6 -Hex) to probe nonpolar interactions, and α-d-mannopyranoside (Na-V 6 -Man) to mimic the protein's natural substrate. Structural and spectroscopic analyses demonstrated that, in contrast to conventional nonhybrid POV clusters which bind nonspecifically to peripheral positively charged protein patches, the hybrid POVs achieve distinct binding behaviors. Specifically, Na-V 6 -N 3 and Na-V 6 -Man selectively target the glycosidic pocket, resembling the binding of the protein's natural substrate, while Na-V 6 -Hex exhibits an unprecedented crystallization of two POV clusters in close proximity, which wrap around the protein surface. These findings highlight that strategic organic functionalization can circumvent electrostatic barriers to achieve site-selective cluster-protein interactions, thus opening new avenues for the application of metal-oxo clusters in biotechnology, drug delivery, and medicine.


  • Organizational Affiliation
    • Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001, Leuven, Belgium.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
Gene Names: LYZ
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1JKF (Subject of Investigation/LOI)
Query on A1JKF

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
Hexavanadate (V6-Hex) polyoxometalate
C24 H38 N8 O21 V6
VXUGKNCLVBNDIT-UHFFFAOYSA-N
MLI
Query on MLI

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
NA
Query on NA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free:  0.163 (Depositor), 0.175 (DCC) 
  • R-Value Work:  0.140 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 0.141 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.583α = 90
b = 76.583β = 90
c = 38.785γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)Belgium--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-01
    Type: Initial release
  • Version 1.1: 2025-12-17
    Changes: Database references