8OKF | pdb_00008okf

WD repeat containing protein 5 (WDR5)- PER2 peptide

• PDB DOI: https://doi.org/10.2210/pdb8OKF/pdb

• Classification: CIRCADIAN CLOCK PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-03-28 Released: 2024-04-10 
• Deposition Author(s): Wolf, E., Boergel, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.201 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

A structural competition involving WDR5 times circadian oscillations

Wolf, E., Boergel, A., Rawleigh, A., Conrady, M., Hof, F., Ricci, K., Brown, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 64.69 kDa 
• Atom Count: 2,538 
• Modeled Residue Count: 314 
• Deposited Residue Count: 570 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase class-mu 26 kDa isozyme,WD repeat domain 5	A	555	Mus musculus	Mutation(s): 0  EC: 2.5.1.18
UniProt
Find proteins for P08515 (Schistosoma japonicum) Explore P08515  Go to UniProtKB:  P08515
Find proteins for P61965 (Mus musculus) Explore P61965  Go to UniProtKB:  P61965
UniProt Groups	P08515P61965

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PER2 peptide	B	15	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O54943 (Mus musculus) Explore O54943  Go to UniProtKB:  O54943
IMPC:  MGI:1195265

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	G [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
144	C [auth A], D [auth A]	TRIS-HYDROXYMETHYL-METHYL-AMMONIUM C4 H12 N O3 DRDCQJADRSJFFD-UHFFFAOYSA-N
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.201 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.152	α = 90
b = 78.152	β = 90
c = 101.748	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-04-10 
Deposition Author(s): Wolf, E., Boergel, A.

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Funding Organization	Location	Grant Number
Not funded	Germany	--

Revision History  

• Version 1.0: 2024-04-10
  Type: Initial release