3RAW | pdb_00003raw

Crystal Structure of human CDC-like kinase 3 isoform in complex with leucettine L41

• PDB DOI: https://doi.org/10.2210/pdb3RAW/pdb

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


• Deposited: 2011-03-28 Released: 2011-05-04 
• Deposition Author(s): Filippakopoulos, P., Fedorov, O., King, O., Debdab, M., Carreaux, F., Renault, S., Bullock, A., Muniz, J.R.C., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Meijer, L., Bazureau, J.P., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.219 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.181 (Depositor) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of human CDC-like kinase 3 isoform with a benzo-dioxol ligand

Filippakopoulos, P., Fedorov, O., King, O., Bullock, A., Muniz, J.R.C., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 90.19 kDa 
• Atom Count: 5,928 
• Modeled Residue Count: 700 
• Deposited Residue Count: 762 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein kinase CLK3	A, B	381	Homo sapiens	Mutation(s): 0  Gene Names: CLK3 EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49761 (Homo sapiens) Explore P49761  Go to UniProtKB:  P49761
PHAROS:  P49761 GTEx:  ENSG00000179335

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3RA	C [auth A], D [auth B]	5-(1,3-benzodioxol-5-ylmethyl)-2-(phenylamino)-4H-imidazol-4-one C17 H13 N3 O3 ZDINVWCJHPMIKS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.219 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.181 (Depositor) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.67	α = 90
b = 122.42	β = 92.6
c = 69.28	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-04 
Deposition Author(s): Filippakopoulos, P., Fedorov, O., King, O., Debdab, M., Carreaux, F., Renault, S., Bullock, A., Muniz, J.R.C., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Meijer, L., Bazureau, J.P., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2011-05-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description