4TZ4

Crystal Structure of Human Cereblon in Complex with DDB1 and Lenalidomide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural Basis for Responsiveness to Thalidomide-Analog Drugs Defined by the Crystal Structure of the Human Cereblon:DDB1:Lenalidomide Complex

Chamberlain, P.P.Wang, M.Riley, M.Delker, S.Carmel, G.Miller, K.Lopez-Girona, A.Pagarigan, B.Leon, B.Rychak, E.Corral, L.Lopez-Girona, A.Ren, Y.Wang, M.Riley, M.Delker, S.Ito, T.Hideki, A.Mori, T.Handa, H.Hakoshima, T.Daniel, T.O.Miller, K.Cathers, B.E.Carmel, G.Pagarigan, B.Leon, B.Rychak, E.Corral, L.Ren, Y.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA damage-binding protein 1
A
1146Homo sapiensMutation(s): 0 
Gene Names: DDB1 (XAP1)
Find proteins for Q16531 (Homo sapiens)
Go to Gene View: DDB1
Go to UniProtKB:  Q16531
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein cereblon
C
381Homo sapiensMutation(s): 0 
Gene Names: CRBN
Find proteins for Q96SW2 (Homo sapiens)
Go to Gene View: CRBN
Go to UniProtKB:  Q96SW2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
LVY
Query on LVY

Download SDF File 
Download CCD File 
C
S-Lenalidomide
C13 H13 N3 O3
GOTYRUGSSMKFNF-JTQLQIEISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.862α = 90.00
b = 129.117β = 90.00
c = 198.677γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
Cootmodel building
HKLdata reduction
HKLdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-06
    Type: Initial release