3P08 | pdb_00003p08

Crystal structure of the human BTK kinase domain

• PDB DOI: https://doi.org/10.2210/pdb3P08/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2010-09-27 Released: 2010-11-03 
• Deposition Author(s): Yu, C.L., Hymowitz, S.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.278 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.222 (Depositor) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

A novel, specific BTK inhibitor antagonizes BCR and FcgR signaling and suppresses inflammatory arthritis

Di Paolo, J., Huang, T., Balazs, M., Barbosa, J., Barck, K.H., Bravo, B., Carano, R.A.D., Darrow, J., Davies, D.R., DeForge, L.E., Diehl, L., Ferrando, R., Gallion, S.L., Gianetti, A.M., Gribling, P., Hurez, V., Hymowitz, S.G., Jones, R., Kropf, J.E., Lee, W.P., Maciejewski, P.M., Mitchell, S.A., Rong, H., Staker, B.L., Whitney, J.A., Yeh, S., Young, W., Yu, C., Zhang, J., Reif, K., Currie, K.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.42 kDa 
• Atom Count: 4,335 
• Modeled Residue Count: 510 
• Deposited Residue Count: 534 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase BTK	A, B	267	Homo sapiens	Mutation(s): 0  Gene Names: AGMX1, ATK, BPK, BTK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q06187 (Homo sapiens) Explore Q06187  Go to UniProtKB:  Q06187
PHAROS:  Q06187 GTEx:  ENSG00000010671

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.278 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.222 (Depositor) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.602	α = 90
b = 103.493	β = 90
c = 117.564	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-03 
Deposition Author(s): Yu, C.L., Hymowitz, S.G.

Revision History  

• Version 1.0: 2010-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description