5AMH

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, trigonal crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structural Dynamics of the Cereblon Ligand Binding Domain.

Hartmann, M.D.Boichenko, I.Coles, M.Lupas, A.N.Hernandez Alvarez, B.

(2015) PLoS One 10: 28342

  • DOI: 10.1371/journal.pone.0128342
  • Primary Citation of Related Structures:  
    5AMH, 5AMI, 5AMJ, 5AMK

  • PubMed Abstract: 
  • Cereblon, a primary target of thalidomide and its derivatives, has been characterized structurally from both bacteria and animals. Especially well studied is the thalidomide binding domain, CULT, which shows an invariable structure across different organisms and in complex with different ligands ...

    Cereblon, a primary target of thalidomide and its derivatives, has been characterized structurally from both bacteria and animals. Especially well studied is the thalidomide binding domain, CULT, which shows an invariable structure across different organisms and in complex with different ligands. Here, based on a series of crystal structures of a bacterial representative, we reveal the conformational flexibility and structural dynamics of this domain. In particular, we follow the unfolding of large fractions of the domain upon release of thalidomide in the crystalline state. Our results imply that a third of the domain, including the thalidomide binding pocket, only folds upon ligand binding. We further characterize the structural effect of the C-terminal truncation resulting from the mental-retardation linked R419X nonsense mutation in vitro and offer a mechanistic hypothesis for its irresponsiveness to thalidomide. At 1.2Å resolution, our data provide a view of thalidomide binding at atomic resolution.


    Organizational Affiliation

    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CEREBLON ISOFORM 4A125Magnetospirillum gryphiswaldense MSR-1Mutation(s): 0 
UniProt
Find proteins for A4TVL0 (Magnetospirillum gryphiswaldense)
Explore A4TVL0 
Go to UniProtKB:  A4TVL0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EF2 (Subject of Investigation/LOI)
Query on EF2

Download Ideal Coordinates CCD File 
C [auth A]S-Thalidomide
C13 H10 N2 O4
UEJJHQNACJXSKW-VIFPVBQESA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
L [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EF2 BindingDB:  5AMH Ki: 4400 (nM) from 1 assay(s)
IC50: 7800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.72α = 90
b = 51.72β = 90
c = 84.71γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release