4TZ4

Crystal Structure of Human Cereblon in Complex with DDB1 and Lenalidomide

• PDB DOI: https://doi.org/10.2210/pdb4TZ4/pdb

• Classification: DNA Binding Protein/Ligase
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-07-09 Released: 2014-08-06 
• Deposition Author(s): Chamberlain, P.P., Pagarigan, B., Delker, S., Leon, B., Riley, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 0.271 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 172.07 kDa 
• Atom Count: 11,081 
• Modelled Residue Count: 1,431 
• Deposited Residue Count: 1,527 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	A	1,146	Homo sapiens	Mutation(s): 0  Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens) Explore Q16531  Go to UniProtKB:  Q16531
GTEx:  ENSG00000167986

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cereblon	B [auth C]	381	Homo sapiens	Mutation(s): 0  Gene Names: CRBN, AD-006
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SW2 (Homo sapiens) Explore Q96SW2  Go to UniProtKB:  Q96SW2
GTEx:  ENSG00000113851

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LVY	D [auth C]	S-Lenalidomide C13 H13 N3 O3 GOTYRUGSSMKFNF-JTQLQIEISA-N
ZN	C	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
LVY	BindingDB:  4TZ4	Ki: min: 1490, max: 1.63e+4 (nM) from 2 assay(s)
		IC50: min: 1500, max: 3.78e+4 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 0.271 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.862	α = 90
b = 129.117	β = 90
c = 198.677	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-06 
Deposition Author(s): Chamberlain, P.P., Pagarigan, B., Delker, S., Leon, B., Riley, M.

Revision History  

• Version 1.0: 2014-08-06
  Type: Initial release
  
• Version 2.0: 2023-12-27
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 2.1: 2024-04-03
  Changes: Refinement description