2JED | pdb_00002jed

The crystal structure of the kinase domain of the protein kinase C theta in complex with NVP-XAA228 at 2.32A resolution.

• PDB DOI: https://doi.org/10.2210/pdb2JED/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2007-01-16 Released: 2008-02-05 
• Deposition Author(s): Stark, W., Bitsch, F., Berner, A., Buelens, F., Graff, P., Depersin, H., Geiser, M., Knecht, R., Rahuel, J., Rummel, G., Schlaeppi, J.M., Schmitz, R., Strauss, A., Wagner, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.221 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

The Crystal Structure of the Kinase Domain of the Protein Kinase C Theta in Complex with Nvp-Xaa228

Stark, W., Bitsch, F., Berner, A., Buelens, F., Graff, P., Depersin, H., Fendrich, G., Geiser, M., Knecht, R., Rahuel, J., Rummel, G., Schlaeppi, J.M., Schmitz, R., Strauss, A., Wagner, J.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 84.67 kDa 
• Atom Count: 5,884 
• Modeled Residue Count: 648 
• Deposited Residue Count: 704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN KINASE C THETA	A, B	352	Homo sapiens	Mutation(s): 2  EC: 2.7.11.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q04759 (Homo sapiens) Explore Q04759  Go to UniProtKB:  Q04759
PHAROS:  Q04759 GTEx:  ENSG00000065675

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LG8	C [auth A], D [auth B]	3-(8-DIMETHYLAMINOMETHYL-6,7,8,9-TETRAHYDRO-PYRIDO[1,2-A]INDOL-10-YL)-4-(1-METHYL-1H-INDOL-3-YL)-PYRROLE-2,5-DIONE C28 H28 N4 O2 OYDDKWPGAIBVKO-JQQWWDHGSA-O
MPD	E [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.221 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.172	α = 90
b = 152.172	β = 90
c = 74.837	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-05 
Deposition Author(s): Stark, W., Bitsch, F., Berner, A., Buelens, F., Graff, P., Depersin, H., Geiser, M., Knecht, R., Rahuel, J., Rummel, G., Schlaeppi, J.M., Schmitz, R., Strauss, A., Wagner, J.

Revision History  

• Version 1.0: 2008-02-05
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-05-15
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.4: 2019-09-25
  Changes: Data collection, Experimental preparation, Other
• Version 1.5: 2023-12-13
  Changes: Data collection, Database references, Refinement description
• Version 1.6: 2024-10-23
  Changes: Structure summary