Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Hetero 12-mer - A4B4C4 

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

Macromolecule Content

• Total Structure Weight: 61279.66 
• Atom Count: 4216 
• Residue Count: 555 
• Unique protein chains: 3

2JK5

Potassium Channel KcsA in complex with Tetrabutylammonium in high K

• DOI: 10.2210/pdb2JK5/pdb

• Classification: IMMUNE SYSTEM/METAL TRANSPORT
• Organism(s): Streptomyces lividans
• Expression System: Mus musculus, Escherichia coli


• Deposited: 2008-08-15 Released: 2009-11-17 
• Deposition Author(s): Lenaeus, M.J., Focia, P.J., Wagner, T., Gross, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.249 
• R-Value Work: 0.202 

Literature

Structures of Kcsa in Complex with Symmetrical Quaternary Ammonium Compounds Reveal a Hydrophobic Binding Site.

Lenaeus, M.J., Burdette, D., Wagner, T., Focia, P.J., Gross, A.

(2014) Biochemistry 53: 5365

• PubMed: 25093676 
• DOI: 10.1021/bi500525s
• Primary Citation of Related Structures:  
  4UUJ, 2W0F


• PubMed Abstract: 
  

Potassium channels allow for the passive movement of potassium ions across the cell membrane and are instrumental in controlling the membrane potential in all cell types. Quaternary ammonium (QA) compounds block potassium channels and have long been used to study the functional and structural properties of these channels. Here we describe the interaction between three symmetrical hydrophobic QAs and the prokaryotic potassium channel KcsA. The structures demonstrate the presence of a hydrophobic pocket between the inner helices of KcsA and provide insight into the binding site and blocking mechanism of hydrophobic QAs. The structures also reveal a structurally hidden pathway between the central cavity and the outside membrane environment reminiscent of the lateral fenestration observed in sodium channels that can be accessed through small conformational changes in the pore wall. We propose that the hydrophobic binding pocket stabilizes the alkyl chains of long-chain QA molecules and may play a key role in hydrophobic drug binding in general.

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Organizational Affiliation: 

Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Medical School , 303 East Chicago Avenue, Chicago, Illinois 60611, United States.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ANTIBODY FAB FRAGMENT LIGHT CHAIN	A	219	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
ANTIBODY FAB FRAGMENT HEAVY CHAIN	B	212	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
VOLTAGE-GATED POTASSIUM CHANNEL	C	124	Streptomyces lividans	Mutation(s): 0  Gene Names: kcsA (skc1)
Membrane protein mpstruct	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Channels: Potassium, Sodium, & Proton Ion-Selective	Protein:  KcsA Potassium channel, H+ gated
Find proteins for P0A334 (Streptomyces lividans) Go to UniProtKB:  P0A334

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K	C	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
TBA	C	TETRABUTYLAMMONIUM ION C16 H36 N DZLFLBLQUQXARW-UHFFFAOYSA-N
L2C	C	(2S)-3-HYDROXY-2-(NONANOYLOXY)PROPYL LAURATE C24 H46 O5 MYFVXYUACRBWGD-QFIPXVFZSA-N
HP6	C	HEPTANE C7 H16 IMNFDUFMRHMDMM-UHFFFAOYSA-N
F09	C	NONAN-1-OL C9 H20 O ZWRUINPWMLAQRD-UHFFFAOYSA-N
CO	C	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.249 
• R-Value Work: 0.202 
• Space Group: I 4

Unit Cell:

Length (Å)	Angle (°)
a = 156.145	α = 90.00
b = 156.145	β = 90.00
c = 76.326	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-08-15 
• Released Date: 2009-11-17 
• Deposition Author(s): Lenaeus, M.J., Focia, P.J., Wagner, T., Gross, A.

Revision History 

• Version 1.0: 2009-11-17
  Type: Initial release
• Version 1.1: 2014-08-27
  Type: Database references, Derived calculations, Other, Source and taxonomy, Structure summary, Version format compliance
• Version 1.2: 2014-09-03
  Type: Database references