Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 135.48 kDa 
• Atom Count: 9391 
• Modelled Residue Count: 1143 
• Deposited Residue Count: 1174 
• Unique protein chains: 3

2CCI

Crystal structure of phospho-CDK2 Cyclin A in complex with a peptide containing both the substrate and recruitment sites of CDC6

• PDB DOI: 10.2210/pdb2CCI/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-01-16 Released: 2006-05-03 
• Deposition Author(s): Cheng, K.Y., Noble, M.E.M., Skamnaki, V., Brown, N.R., Lowe, E.D., Kontogiannis, L., Shen, K., Cole, P.A., Siligardi, G., Johnson, L.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.321 
• R-Value Work: 0.261 
• R-Value Observed: 0.264 

Literature

The role of the phospho-CDK2/cyclin A recruitment site in substrate recognition.

Cheng, K.Y., Noble, M.E., Skamnaki, V., Brown, N.R., Lowe, E.D., Kontogiannis, L., Shen, K., Cole, P.A., Siligardi, G., Johnson, L.N.

(2006) J Biol Chem 281: 23167-23179

• PubMed: 16707497 
• DOI: 10.1074/jbc.M600480200
• Primary Citation of Related Structures:  
  2CCH, 2CCI


• PubMed Abstract: 
  

Phospho-CDK2/cyclin A, a kinase that is active in cell cycle S phase, contains an RXL substrate recognition site that is over 40 A from the catalytic site. The role of this recruitment site, which enhances substrate affinity and catalytic efficiency, has been investigated using peptides derived from the natural substrates, namely CDC6 and p107, and a bispeptide inhibitor in which the gamma-phosphate of ATP is covalently attached by a linker to the CDC6 substrate peptide. X-ray studies with a 30-residue CDC6 peptide in complex with pCDK2/cyclin A showed binding of a dodecamer peptide at the recruitment site and a heptapeptide at the catalytic site, but no density for the linking 11 residues. Kinetic studies established that the CDC6 peptide had an 18-fold lower Km compared with heptapeptide substrate and that this effect required the recruitment peptide to be covalently linked to the substrate peptide. X-ray studies with the CDC6 bispeptide showed binding of the dodecamer at the recruitment site and the modified ATP in two alternative conformations at the catalytic site. The CDC6 bispeptide was a potent inhibitor competitive with both ATP and peptide substrate of pCDK2/cyclin A activity against a heptapeptide substrate (Ki = 0.83 nm) but less effective against RXL-containing substrates. We discuss how localization at the recruitment site (KD 0.4 microm) leads to increased catalytic efficiency and the design of a potent inhibitor. The notion of a flexible linker between the sites, which must have more than a minimal number of residues, provides an explanation for recognition and discrimination against different substrates.

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Organizational Affiliation: 

Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	A, C	299	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-A2	B, D	258	Homo sapiens	Mutation(s): 0  Gene Names: CCNA2, CCN1, CCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P20248 (Homo sapiens) Explore P20248  Go to UniProtKB:  P20248
PHAROS:  P20248 GTEx:  ENSG00000145386

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division control protein 6 homolog	E [auth F], F [auth I]	30	Homo sapiens	Mutation(s): 4  Gene Names: CDC6, CDC18L
UniProt & NIH Common Fund Data Resources
Find proteins for Q99741 (Homo sapiens) Explore Q99741  Go to UniProtKB:  Q99741
PHAROS:  Q99741 GTEx:  ENSG00000094804

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	G [auth A], I [auth C]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	H [auth A], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.321 
• R-Value Work: 0.261 
• R-Value Observed: 0.264 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.42	α = 90
b = 114.389	β = 90
c = 170.709	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-01-16 
• Released Date: 2006-05-03 
Deposition Author(s): Cheng, K.Y., Noble, M.E.M., Skamnaki, V., Brown, N.R., Lowe, E.D., Kontogiannis, L., Shen, K., Cole, P.A., Siligardi, G., Johnson, L.N.

Revision History  

• Version 1.0: 2006-05-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-06-06
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary