9I69

Crystal structure of human Cdc20 bound to synthetic D-box peptide D20

• PDB DOI: https://doi.org/10.2210/pdb9I69/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2025-01-29 Released: 2025-02-12 
• Deposition Author(s): Eapen, R., Okoye, C., Stubbs, C., Schimpl, M., Tischer, T., Fisher, E.J., Zacharopoulou, M., Ferrer, F., Barford, D., Spring, D., Lindon, C., Phillips, C., Itzhaki, L.S.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 
  0.184 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Development of D-box peptides to inhibit the Anaphase Promoting Complex/Cyclosome

Eapen, R., Okoye, C., Stubbs, C., Schimpl, M., Tischer, T., Fisher, E.J., Zacharopoulou, M., Ferrer, F., Barford, D., Spring, D., Lindon, C., Phillips, C., Itzhaki, L.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: 55.8 kDa 
• Atom Count: 2,720 
• Modelled Residue Count: 317 
• Deposited Residue Count: 508 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division cycle protein 20 homolog	A	499	Homo sapiens	Mutation(s): 0  Gene Names: CDC20
UniProt & NIH Common Fund Data Resources
Find proteins for Q12834 (Homo sapiens) Explore Q12834  Go to UniProtKB:  Q12834
PHAROS:  Q12834 GTEx:  ENSG00000117399

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ARG-ALA-PRO-0JY-SER-ASP	B	9	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free:  0.184 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.339	α = 90
b = 87.341	β = 110.14
c = 48.511	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Eapen, R., Okoye, C., Stubbs, C., Schimpl, M., Tischer, T., Fisher, E.J., Zacharopoulou, M., Ferrer, F., Barford, D., Spring, D., Lindon, C., Phillips, C., Itzhaki, L.S.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R004137/1

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release