8RTJ | pdb_00008rtj

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

PDB DOI: https://doi.org/10.2210/pdb8RTJ/pdb

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

Deposited: 2024-01-26 Released: 2025-02-12
Deposition Author(s): Paolillo, M., Ferraro, G., Merlino, A.
Funding Organization(s): University of Naples Federico II

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.27 Å
R-Value Free:
0.197 (Depositor), 0.202 (DCC)
R-Value Work:
0.174 (Depositor), 0.180 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

PubMed: 38923243 Search on PubMed
DOI: https://doi.org/10.1002/chem.202401712
Primary Citation Related Structures:
8RTJ, 8RTK

PubMed Abstract:
The binding of the potential drug [V ^IVO(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 ^IVO(8-HQ)(H ₂O)] ⁺ and [V ^IVO(8-HQ) ₂(H ₂O)] 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 ^IVO(8-HQ)(H ₂O)] ⁺ interacts covalently with the solvent exposed Asp119, while cis-[V ^IVO(8-HQ) ₂(H ₂O)] non-covalently with Arg128 and Lys96 from a symmetry mate. The covalent binding of [V ^IVO(8-HQ)(H ₂O)] ⁺ 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 ^VO 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: 15.19 kDa
Atom Count: 1,248
Modeled Residue Count: 129
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A [auth AAA]	129	Gallus gallus	Mutation(s): 0 EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I3Y (Subject of Investigation/LOI) Query on I3Y Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain C [auth AAA]	C [auth AAA]	2,2-bis($l^{1}-oxidanyl)-3-oxa-1$l^{4}-aza-2$l^{4}-vanadatricyclo[6.3.1.0^{4,12}]dodeca-1(12),4,6,8,10-pentaene C₉ H₈ N O₃ V VHSPINZPWRCWRI-UHFFFAOYSA-K		Interactions Focus chain C [auth AAA] Interactions & Density Focus chain C [auth AAA]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain M [auth AAA] SDF format, chain L [auth AAA] SDF format, chain K [auth AAA] SDF format, chain J [auth AAA] SDF format, chain I [auth AAA] SDF format, chain H [auth AAA] SDF format, chain G [auth AAA] SDF format, chain F [auth AAA] SDF format, chain E [auth AAA] MOL2 format, chain M [auth AAA] MOL2 format, chain L [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain E [auth AAA] mmCIF format, chain M [auth AAA] mmCIF format, chain L [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain E [auth AAA]	E [auth AAA] F [auth AAA] G [auth AAA] H [auth AAA] I [auth AAA] E [auth AAA], F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA], J [auth AAA], K [auth AAA], L [auth AAA], M [auth AAA]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain M [auth AAA] Interactions & Density Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain M [auth AAA]
V Query on V Download:Ideal Coordinates CCD File SDF format, chain D [auth AAA] MOL2 format, chain D [auth AAA] mmCIF format, chain D [auth AAA]	D [auth AAA]	VANADIUM ION V KOKKJWHERHSKEB-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Interactions & Density Focus chain D [auth AAA]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain B [auth AAA] MOL2 format, chain B [auth AAA] mmCIF format, chain B [auth AAA]	B [auth AAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth AAA] Interactions & Density Focus chain B [auth AAA]