8RTK | pdb_00008rtk

X-ray structure of lysozyme obtained upon reaction with [VIVO(8-HQ)2] in sodium formate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 
    0.192 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.179 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Protein-Protein Stabilization in V IV O/8-Hydroxyquinoline-Lysozyme Adducts.

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

(2024) Chemistry 30: e202401712-e202401712

  • DOI: https://doi.org/10.1002/chem.202401712
  • Primary Citation Related Structures: 
    8RTJ, 8RTK

  • PubMed Abstract: 

    The binding of the potential drug [V IV O(8-HQ) 2 ], where 8-HQ is 8-hydroxyquinolinato, with hen egg white lysozyme (HEWL) was evaluated through spectroscopic (electron paramagnetic resonance, EPR, and UV-visible), spectrometric (electrospray ionization-mass spectrometry, ESI-MS), crystallographic (X-ray diffraction, XRD), and computational (DFT and docking) studies. ESI-MS indicates the interaction of [V IV O(8-HQ)(H 2 O)] + and [V IV O(8-HQ) 2 (H 2 O)] species with HEWL. Room temperature EPR spectra suggest both covalent and non-covalent binding of the two different V-containing fragments. XRD analyses confirm these findings, showing that [V IV O(8-HQ)(H 2 O)] + interacts covalently with the solvent exposed Asp119, while cis-[V IV O(8-HQ) 2 (H 2 O)] non-covalently with Arg128 and Lys96 from a symmetry mate. The covalent binding of [V IV O(8-HQ)(H 2 O)] + to Asp119 is favored by a π-π contact with Trp62 and a H-bond with Asn103 of a symmetry-related molecule. Additionally, the covalent binding of V V O 2 + to Asp48 and non-covalent binding of other V-containing fragments to Arg5, Cys6, and Glu7 are revealed. Molecular docking indicates that, in the absence of the interactions occurring at the protein-protein interface close to Asp119, the covalent binding to Glu35 or Asp52 should be preferred. Such a protein-protein stabilization could be more common than what believed up today, at least in the solid state, and should be considered in the characterization of metal-protein adducts.


  • Organizational Affiliation
    • Department of Chemical Sciences, University of Naples 'Federico II', Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Napoli, Italy.

Macromolecule Content 

  • Total Structure Weight: 15.16 kDa 
  • Atom Count: 1,284 
  • Modeled Residue Count: 129 
  • Deposited Residue Count: 129 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
A1H23
(Subject of Investigation/LOI)

Query on A1H23



Download:Ideal Coordinates CCD File
C [auth AAA]2-$l^{1}-oxidanyl-2,2'-spirobi[3-oxa-1$l^{4}-aza-2$l^{7}-vanadatricyclo[6.3.1.0^{4,12}]dodeca-1(12),4,6,8,10-pentaene] 2-oxide
C18 H12 N2 O4 V
OZVTWOAUPDJZJU-UHFFFAOYSA-L
EPE

Query on EPE



Download:Ideal Coordinates CCD File
B [auth AAA]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
VVB
(Subject of Investigation/LOI)

Query on VVB



Download:Ideal Coordinates CCD File
E [auth AAA]bis(oxidanyl)vanadium
H2 O2 V
UVEFAEMXFFXFKB-UHFFFAOYSA-L
VVO
(Subject of Investigation/LOI)

Query on VVO



Download:Ideal Coordinates CCD File
D [auth AAA],
F [auth AAA]
oxovanadium(2+)
O V
MHHDXUNFNAZUGB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free:  0.192 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.179 (DCC) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.08α = 90
b = 77.08β = 90
c = 37.53γ = 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
University of Naples Federico IIItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Database references