1BWN

PH DOMAIN AND BTK MOTIF FROM BRUTON'S TYROSINE KINASE MUTANT E41K IN COMPLEX WITH INS(1,3,4,5)P4

• PDB DOI:  https://doi.org/10.2210/pdb1BWN/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 1998-09-25 Released: 1999-06-15 
• Deposition Author(s): Djinovic Carugo, K., Baraldi, E., Hyvoenen, M., Lo Surdo, P., Riley, A., Potter, B., Saraste, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.290 
• R-Value Work: 0.214 

Literature

Structure of the PH domain from Bruton's tyrosine kinase in complex with inositol 1,3,4,5-tetrakisphosphate.

Baraldi, E., Carugo, K.D., Hyvonen, M., Surdo, P.L., Riley, A.M., Potter, B.V., O'Brien, R., Ladbury, J.E., Saraste, M.

(1999) Structure 7: 449-460

• PubMed: 10196129 
• DOI: https://doi.org/10.1016/s0969-2126(99)80057-4
• Primary Citation of Related Structures:  
  1B55, 1BWN


• PubMed Abstract: 
  

The activity of Bruton's tyrosine kinase (Btk) is important for the maturation of B cells. A variety of point mutations in this enzyme result in a severe human immunodeficiency known as X-linked agammaglobulinemia (XLA). Btk contains a pleckstrin-homology (PH) domain that specifically binds phosphatidylinositol 3,4,5-trisphosphate and, hence, responds to signalling via phosphatidylinositol 3-kinase. Point mutations in the PH domain might abolish membrane binding, preventing signalling via Btk.

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Organizational Affiliation: 

European Molecular Biology Laboratory, Meyerhofstrasse 1, Postfach 102209, D-69012 Heidelberg, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.1 kDa 
• Atom Count: 3,101 
• Modelled Residue Count: 327 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BRUTON'S TYROSINE KINASE	A, B	169	Homo sapiens	Mutation(s): 1  Gene Names: BTK, AGMX1, ATK, BPK EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (UniProt) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q06187 (Homo sapiens) Explore Q06187  Go to UniProtKB:  Q06187
PHAROS:  Q06187

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4IP	D [auth A], E [auth A], G [auth B], H [auth B]	INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE C6 H16 O18 P4 CIPFCGZLFXVXBG-CNWJWELYSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4IP	PDBBind:  1BWN	Kd: 87 (nM) from 1 assay(s)
	Binding MOAD:  1BWN	Kd: 87 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.290 
• R-Value Work: 0.214 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.784	α = 90
b = 110.784	β = 90
c = 215.6	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-06-15 
Deposition Author(s): Djinovic Carugo, K., Baraldi, E., Hyvoenen, M., Lo Surdo, P., Riley, A., Potter, B., Saraste, M.

Revision History  

• Version 1.0: 1999-06-15
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations