8RQA

Crystal structure of CRBN-midi in complex with Lenalidomide

PDB DOI: https://doi.org/10.2210/pdb8RQA/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-01-17 Released: 2024-09-25
Deposition Author(s): Rutter, Z.J., Kroupova, A., Zollman, D., Ciulli, A.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.342
R-Value Work: 0.300
R-Value Observed: 0.302

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders

Kroupova, A., Spiteri, V., Furihata, H., Darren, D., Ramachandran, S., Rutter, Z.J., Chakraborti, S., Haubrich, K., Pethe, J., Gonzales, D., Wijaya, A., Rodriguez-Rios, M., Lynch, D., Farnaby, W., Nakasone, M., Zollman, D., Ciulli, A.

To be published.

Macromolecule Content

Total Structure Weight: 37.8 kDa
Atom Count: 2,292
Modelled Residue Count: 306
Deposited Residue Count: 329
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cereblon	A	329	Homo sapiens	Mutation(s): 12 Gene Names: CRBN, AD-006
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SW2 (Homo sapiens) Explore Q96SW2 Go to UniProtKB: Q96SW2
PHAROS: Q96SW2 GTEx: ENSG00000113851
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96SW2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LVY (Subject of Investigation/LOI) Query on LVY Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	S-Lenalidomide C₁₃ H₁₃ N₃ O₃ GOTYRUGSSMKFNF-JTQLQIEISA-N		Interactions Focus chain B [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.342
R-Value Work: 0.300
R-Value Observed: 0.302
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.989	α = 90
b = 95.717	β = 90
c = 148.252	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2024-09-25
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.