7Q0V

Lysozyme soaked with V(IV)OSO4 and phen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Binding of V IV O 2+ , V IV OL, V IV OL 2 and V V O 2 L Moieties to Proteins: X-ray/Theoretical Characterization and Biological Implications.

Santos, M.F.A.Sciortino, G.Correia, I.Fernandes, A.C.P.Santos-Silva, T.Pisanu, F.Garribba, E.Costa Pessoa, J.

(2022) Chemistry 28: e202200105-e202200105

  • DOI: https://doi.org/10.1002/chem.202200105
  • Primary Citation of Related Structures:  
    7Q0T, 7Q0U, 7Q0V, 7Q0W, 7Q0X

  • PubMed Abstract: 

    Vanadium compounds have frequently been proposed as therapeutics, but their application has been hampered by the lack of information on the different V-containing species that may form and how these interact with blood and cell proteins, and with enzymes. Herein, we report several resolved crystal structures of lysozyme with bound V IV O 2+ and V IV OL 2+ , where L=2,2'-bipyridine or 1,10-phenanthroline (phen), and of trypsin with V IV O(picolinato) 2 and V V O 2 (phen) + moieties. Computational studies complete the refinement and shed light on the relevant role of hydrophobic interactions, hydrogen bonds, and microsolvation in stabilizating the structure. Noteworthy is that the trypsin-V V O 2 (phen) and trypsin-V IV O(OH)(phen) adducts correspond to similar energies, thus suggesting a possible interconversion under physiological/biological conditions. The obtained data support the relevance of hydrolysis of V IV and V V complexes in the several types of binding established with proteins and the formation of different adducts that might contribute to their pharmacological action, and significantly widen our knowledge of vanadium-protein interactions.


  • Organizational Affiliation

    Centro de Química Estrutural and Departamento de Engenharia Química, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme129Gallus 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 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PHN (Subject of Investigation/LOI)
Query on PHN

Download Ideal Coordinates CCD File 
B [auth A]1,10-PHENANTHROLINE
C12 H8 N2
DGEZNRSVGBDHLK-UHFFFAOYSA-N
ACT
Query on ACT

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O [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
V (Subject of Investigation/LOI)
Query on V

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
VANADIUM ION
V
KOKKJWHERHSKEB-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

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H [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
O
Query on O

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G [auth A]OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.68α = 90
b = 77.68β = 90
c = 37.757γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugal--

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-25
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references
  • Version 1.2: 2022-06-15
    Changes: Database references
  • Version 1.3: 2022-07-27
    Changes: Database references
  • Version 1.4: 2024-01-31
    Changes: Data collection, Refinement description