8GI4

Crystal structure of human LIMK2 PDZ domain

• PDB DOI: https://doi.org/10.2210/pdb8GI4/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-03-13 Released: 2023-12-06 
• Deposition Author(s): Casanova Sepulveda, G., Boggon, T.J.
• Funding Organization(s): American Heart Association, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.234 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 

Literature

Autoregulation of the LIM kinases by their PDZ domain

Casanova-Sepulveda, G., Sexton, J.A., Turk, B.E., Boggon, T.J.

(2023) Nat Commun 14: 8441

• DOI: https://doi.org/10.1038/s41467-023-44148-4

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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Biological Assembly 7  

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

Biological assembly 7 assigned by authors.

Biological Assembly 8  

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

Biological assembly 8 assigned by authors.

Macromolecule Content

• Total Structure Weight: 109.83 kDa 
• Atom Count: 6,091 
• Modelled Residue Count: 750 
• Deposited Residue Count: 984 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIM domain kinase 2	A, B, C, D, E, F, G, H	123	Homo sapiens	Mutation(s): 1  Gene Names: LIMK2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P53671 (Homo sapiens) Explore P53671  Go to UniProtKB:  P53671
PHAROS:  P53671 GTEx:  ENSG00000182541

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.234 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.15785/SBGRID/1010

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.95	α = 90
b = 83.028	β = 96.58
c = 83.08	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-06 
Deposition Author(s): Casanova Sepulveda, G., Boggon, T.J.

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Funding Organization	Location	Grant Number
American Heart Association	United States	835293
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM102262
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM138411

Revision History  

• Version 1.0: 2023-12-06
  Type: Initial release
  
• Version 1.1: 2023-12-27
  Changes: Database references