2JC6 | pdb_00002jc6

Crystal structure of human calmodulin-dependent protein kinase 1D

• PDB DOI: https://doi.org/10.2210/pdb2JC6/pdb

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


• Deposited: 2006-12-19 Released: 2007-02-13 
• Deposition Author(s): Debreczeni, J.E., Rellos, P., Fedorov, O., Niesen, F.H., Bhatia, C., Shrestha, L., Salah, E., Smee, C., Colebrook, S., Berridge, G., Gileadi, O., Bunkoczi, G., Ugochukwu, E., Pike, A.C.W., von Delft, F., Knapp, S., Sundstrom, M., Weigelt, J., Arrowsmith, C.H., Edwards, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.248 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human Calmodulin-Dependent Protein Kinase 1D

Debreczeni, J.E., Rellos, P., Fedorov, O., Niesen, F.H., Bhatia, C., Shrestha, L., Salah, E., Smee, C., Colebrook, S., Berridge, G., Gileadi, O., Bunkoczi, G., Ugochukwu, E., Pike, A.C.W., von Delft, F., Knapp, S., Sundstrom, M., Weigelt, J., Arrowsmith, C.H., Edwards, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 76.38 kDa 
• Atom Count: 4,628 
• Modeled Residue Count: 555 
• Deposited Residue Count: 668 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE 1D	A, B [auth C]	334	Homo sapiens	Mutation(s): 0  EC: 2.7.11.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IU85 (Homo sapiens) Explore Q8IU85  Go to UniProtKB:  Q8IU85
PHAROS:  Q8IU85 GTEx:  ENSG00000183049

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QPP	C [auth A], D [auth C]	N-(5-METHYL-1H-PYRAZOL-3-YL)-2-PHENYLQUINAZOLIN-4-AMINE C18 H15 N5 JYCUVOXSZBECAY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.248 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.64	α = 90
b = 93.06	β = 96.16
c = 101.86	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-13 
Deposition Author(s): Debreczeni, J.E., Rellos, P., Fedorov, O., Niesen, F.H., Bhatia, C., Shrestha, L., Salah, E., Smee, C., Colebrook, S., Berridge, G., Gileadi, O., Bunkoczi, G., Ugochukwu, E., Pike, A.C.W., von Delft, F., Knapp, S., Sundstrom, M., Weigelt, J., Arrowsmith, C.H., Edwards, A.

Revision History  

• Version 1.0: 2007-02-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Refinement description, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description