3NR9 | pdb_00003nr9

Structure of human CDC2-like kinase 2 (CLK2)

• PDB DOI: https://doi.org/10.2210/pdb3NR9/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-06-30 Released: 2010-08-25 
• Deposition Author(s): Chaikuad, A., Savitsky, P., Krojer, T., Muniz, J.R.C., Filippakopoulos, P., Rellos, P., Keates, T., Fedorov, O., Pike, A.C.W., Eswaran, J., Berridge, G., Phillips, C., Zhang, Y., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Structure of human CDC2-like kinase 2 (CLK2)

Chaikuad, A., Savitsky, P., Krojer, T., Muniz, J.R.C., Filippakopoulos, P., Rellos, P., Keates, T., Fedorov, O., Pike, A.C.W., Eswaran, J., Berridge, G., Phillips, C., Zhang, Y., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 131.22 kDa 
• Atom Count: 8,562 
• Modelled Residue Count: 1,035 
• Deposited Residue Count: 1,104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein kinase CLK2	A, B, C	368	Homo sapiens	Mutation(s): 0  Gene Names: CLK2 EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49760 (Homo sapiens) Explore P49760  Go to UniProtKB:  P49760
PHAROS:  P49760 GTEx:  ENSG00000176444

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NR9	D [auth A], E [auth B], F [auth C]	(5Z)-5-(quinolin-6-ylmethylidene)-2-[(thiophen-2-ylmethyl)amino]-1,3-thiazol-4(5H)-one C18 H13 N3 O S2 XOLMRFUGOINFDQ-YBEGLDIGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.678	α = 90
b = 97.678	β = 90
c = 223.029	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-25 
Deposition Author(s): Chaikuad, A., Savitsky, P., Krojer, T., Muniz, J.R.C., Filippakopoulos, P., Rellos, P., Keates, T., Fedorov, O., Pike, A.C.W., Eswaran, J., Berridge, G., Phillips, C., Zhang, Y., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description