7Q0V | pdb_00007q0v

Lysozyme soaked with V(IV)OSO4 and phen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 
    0.176 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.147 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.149 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PHNClick on this verticalbar to view details

This is version 1.5 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]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
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 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.147 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.149 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PHNClick on this verticalbar to view details

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
  • Version 1.5: 2024-10-16
    Changes: Structure summary