Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34534.01 
• Atom Count: 2370 
• Residue Count: 299 
• Unique protein chains: 1

1B38

HUMAN CYCLIN-DEPENDENT KINASE 2

• DOI: 10.2210/pdb1B38/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 1998-12-17 Released: 1998-12-23 
• Deposition Author(s): Brown, N.R., Noble, M.E.M., Lawrie, A.M., Morris, M.C., Tunnah, P., Divita, G., Johnson, L.N., Endicott, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.250 
• R-Value Work: 0.180 

Literature

Effects of phosphorylation of threonine 160 on cyclin-dependent kinase 2 structure and activity.

Brown, N.R., Noble, M.E., Lawrie, A.M., Morris, M.C., Tunnah, P., Divita, G., Johnson, L.N., Endicott, J.A.

(1999) J.Biol.Chem. 274: 8746-8756

• PubMed: 10085115 
• Primary Citation of Related Structures:  
  1B39


• PubMed Abstract: 
  

We have prepared phosphorylated cyclin-dependent protein kinase 2 (CDK2) for crystallization using the CDK-activating kinase 1 (CAK1) from Saccharomyces cerevisiae and have grown crystals using microseeding techniques. Phosphorylation of monomeric human CDK2 by CAK1 is more efficient than phosphorylation of the binary CDK2-cyclin A complex. Phosphorylated CDK2 exhibits histone H1 kinase activity corresponding to approximately 0.3% of that observed with the fully activated phosphorylated CDK2-cyclin A complex. Fluorescence measurements have shown that Thr160 phosphorylation increases the affinity of CDK2 for both histone substrate and ATP and decreases its affinity for ADP. By contrast, phosphorylation of CDK2 has a negligible effect on the affinity for cyclin A. The crystal structures of the ATP-bound forms of phosphorylated CDK2 and unphosphorylated CDK2 have been solved at 2.1-A resolution. The structures are similar, with the major difference occurring in the activation segment, which is disordered in phosphorylated CDK2. The greater mobility of the activation segment in phosphorylated CDK2 and the absence of spontaneous crystallization suggest that phosphorylated CDK2 may adopt several different mobile states. The majority of these states are likely to correspond to inactive conformations, but a small fraction of phosphorylated CDK2 may be in an active conformation and hence explain the basal activity observed.

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Related Citations: 

• Multiple Modes of Ligand Recognition: Crystal Structures of Cyclin-Dependent Protein Kinase 2 in Complex with ATP and Two Inhibitors, Olomoucine and Isopentenyladenine
  Schulze-Gahmen, U.,Brandsen, J.,Jones, H.D.,Morgan, D.O.,Meijer, L.,Vesely, J.,Kim, S.H.
  (1995) Proteins 22: 378




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Organizational Affiliation: 

Laboratory of Molecular Biophysics, Department of Biochemistry, and Oxford Centre for Molecular Sciences, University of Oxford, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, United Kingdom.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (CELL DIVISION PROTEIN KINASE 2)	A	299	Homo sapiens	Mutation(s): 0  Gene Names: CDK2 (CDKN2) EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens) Go to Gene View: CDK2 Go to UniProtKB:  P24941

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ATP	A	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ACE	A	NON-POLYMER	C2 H4 O		--

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ATP	Kd: 254 nM BINDINGMOAD
ATP	Kd: 254 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.250 
• R-Value Work: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 53.333	α = 90.00
b = 71.122	β = 90.00
c = 72.190	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-12-17 
• Released Date: 1998-12-23 
• Deposition Author(s): Brown, N.R., Noble, M.E.M., Lawrie, A.M., Morris, M.C., Tunnah, P., Divita, G., Johnson, L.N., Endicott, J.A.

Revision History 

• Version 1.0: 1998-12-23
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance