X-ray structure of human ubiquitin Cd(II) adduct

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.279 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structural probing of Zn(II), Cd(II) and Hg(II) binding to human ubiquitin.

Falini, G.Fermani, S.Tosi, G.Arnesano, F.Natile, G.

(2008) Chem Commun (Camb) 45: 5960-5962

  • DOI: https://doi.org/10.1039/b813463d
  • Primary Citation of Related Structures:  
    3EEC, 3EFU, 3EHV

  • PubMed Abstract: 

    A structural investigation performed on adducts of human ubiquitin with group-12 metal ions reveals common preferential anchoring sites, the most populated one being His68; at higher metal ion concentration a second and a third site, close to the N-terminus of the protein, become populated and promote a polymorphic transition from orthorhombic to cubic form; Glu16 and Glu18, involved in the latter metal binding, undergo a remarkable displacement from their position in native ubiquitin; the aggregate stereochemistry appears to be driven by the clustering of deshielded backbone hydrogen-bond patches, and metal ions foster this process.

  • Organizational Affiliation

    Dipartimento di Chimica, G. Ciamician, Università di Bologna, via Selmi 2, 40126, Bologna, Italy. giuseppe.falini@unibo.it

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
76Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
GTEx:  ENSG00000150991 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG48
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CD

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.279 
  • Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.253α = 90
b = 105.253β = 90
c = 105.253γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-12-11
    Changes: Data collection
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description