9ET6 | pdb_00009et6

CDK2-cyclin A in complex with FragLite 7

• PDB DOI: https://doi.org/10.2210/pdb9ET6/pdb

• Classification: CELL CYCLE
• Organism(s): Bos taurus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-03-26 Released: 2025-04-09 
• Deposition Author(s): Hope, I., Martin, M.P., Waring, M.J., Noble, M.E.M., Endicott, J.A., Tatum, N.J.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom), Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.239 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.209 (DCC) 

Starting Model: experimental

Literature

Crystallographic fragment screening of CDK2-cyclin A: FragLites map sites of protein-protein interaction

Hope, I., Martin, M.P., Waring, M.J., Noble, M.E.M., Endicott, J.A., Tatum, N.J.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 132.78 kDa 
• Atom Count: 9,320 
• Modelled Residue Count: 1,123 
• Deposited Residue Count: 1,140 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-A2	A [auth D], C [auth B]	268	Bos taurus	Mutation(s): 0  Gene Names: CCNA2
UniProt
Find proteins for P30274 (Bos taurus) Explore P30274  Go to UniProtKB:  P30274

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	B [auth A], D [auth C]	302	Homo sapiens	Mutation(s): 0  Gene Names: CDK2, CDKN2 EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens) Explore P24941  Go to UniProtKB:  P24941
PHAROS:  P24941 GTEx:  ENSG00000123374

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HHQ (Subject of Investigation/LOI)	E [auth D], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth C], O [auth C]	4-iodanyl-3~{H}-pyridin-2-one C5 H4 I N O GRVSGGNZRNHMQI-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	B [auth A], D [auth C]	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.239 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.209 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.252	α = 90
b = 133.568	β = 90
c = 147.658	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-09 
Deposition Author(s): Hope, I., Martin, M.P., Waring, M.J., Noble, M.E.M., Endicott, J.A., Tatum, N.J.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N009738/1
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/V029142/1
Cancer Research UK	United Kingdom	C2115/A21421

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release