7R1Q | pdb_00007r1q

X-ray structure of the adduct formed upon reaction of the gold(I) N-heterocyclic carbene complex Au2 with lysozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 
    0.170 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.132 (Depositor), 0.132 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Halo complexes of gold(I) containing glycoconjugate carbene ligands: synthesis, characterization, cytotoxicity and interaction with proteins and DNA model systems.

Annunziata, A.Ferraro, G.Cucciolito, M.E.Imbimbo, P.Tuzi, A.Monti, D.M.Merlino, A.Ruffo, F.

(2022) Dalton Trans 51: 10475-10485

  • DOI: https://doi.org/10.1039/d2dt00423b
  • Primary Citation Related Structures: 
    7R1P, 7R1Q

  • PubMed Abstract: 

    New neutral carbene complexes of gold(I) [Au(Im-Me)X] (X = Cl, Au1; X = Br, Au2; X = I, Au3) have been synthesized and fully characterized by different techniques, including NMR and UV-vis absorption spectroscopy and single crystal X-ray diffraction. The carbene ligand Im-Me is decorated with a glucoside fragment via a triazole linker, obtainable through a click chemistry reaction. The compounds retain the Au-NHC fragment in aqueous solvents, and an equilibrium between the neutral halo- and the cationic di-carbene form [Au(Im-Me) 2 ] + is observed, whose extent follows the trend Au1 < Au2 < Au3. Cytotoxicity studies on two cancer and two non-tumorigenic cell lines reflect the solution behavior, as a certain difference among the complexes was disclosed, with the iodo complex Au3 being more active and selective. The compounds interact with both DNA and protein model systems. The X-ray structure of the adduct formed upon the reaction of Au1 with bovine pancreatic ribonuclease (RNase A) reveals Au binding at the side chain of His105 of both protein molecules A and B of the asymmetric unit. The binding of gold atoms at both the nitrogen atoms of the imidazole ring of His15 and at the N-terminal tail has been found in the adduct formed with hen egg white lysozyme.


  • Organizational Affiliation
    • Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia 21, 80126, Napoli, Italy. dariamaria.monti@unina.it.

Macromolecule Content 

  • Total Structure Weight: 15 kDa 
  • Atom Count: 1,370 
  • 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
LysozymeA [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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free:  0.170 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.132 (Depositor), 0.132 (DCC) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77α = 90
b = 77β = 90
c = 37.27γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2022-07-20
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary