4MLP

Mammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase

• PDB DOI: https://doi.org/10.2210/pdb4MLP/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2013-09-06 Released: 2013-10-16 
• Deposition Author(s): Nangle, S., Xing, W., Zheng, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.217 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Starting Model: experimental

Literature

Crystal structure of mammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase.

Nangle, S., Xing, W., Zheng, N.

(2013) Cell Res 23: 1417-1419

• PubMed: 24080726 
• DOI: https://doi.org/10.1038/cr.2013.136
• Primary Citation of Related Structures:  
  4MLP

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Organizational Affiliation: 

Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 236.35 kDa 
• Atom Count: 17,726 
• Modelled Residue Count: 1,968 
• Deposited Residue Count: 2,048 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cryptochrome-2	A [auth C], B [auth A], C [auth B], D	512	Mus musculus	Mutation(s): 0  Gene Names: Cry2, Kiaa0658
UniProt
Find proteins for Q9R194 (Mus musculus) Explore Q9R194  Go to UniProtKB:  Q9R194

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2CX	E [auth C], F [auth A], G [auth B], H [auth D]	N-[(2S)-3-(9H-carbazol-9-yl)-2-hydroxypropyl]-N-(furan-2-ylmethyl)methanesulfonamide C21 H22 N2 O4 S OQAFDLPAPSSOHY-MRXNPFEDSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2CX	BindingDB:  4MLP	EC50: 870 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.217 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.21	α = 89.94
b = 93.651	β = 90.09
c = 141.179	γ = 90.25

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-16 
Deposition Author(s): Nangle, S., Xing, W., Zheng, N.

Revision History  

• Version 1.0: 2013-10-16
  Type: Initial release
  
• Version 1.1: 2013-12-18
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description