5KXI

X-ray structure of the human Alpha4Beta2 nicotinic receptor

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 
  • Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc

  • Deposited: 2016-07-20 Released: 2016-09-28 
  • Deposition Author(s): Morales-Perez, C.L., Noviello, C.M., Hibbs, R.E.
  • Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA), Welch Foundation, McKnight Scholar Award, Klingenstein-Simons Fellowship Award

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.94 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.285 
  • R-Value Observed: 0.286 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history. 



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neuronal acetylcholine receptor subunit alpha-4
A, D
386Homo sapiensMutation(s): 0 
Gene Names: CHRNA4, NACRA4
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P43681 (Homo sapiens)
Explore P43681 
Go to UniProtKB:  P43681
PHAROS:  P43681
GTEx:  ENSG00000101204 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43681
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Neuronal acetylcholine receptor subunit beta-2
B, C, E
403Homo sapiensMutation(s): 0 
Gene Names: CHRNB2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P17787 (Homo sapiens)
Explore P17787 
Go to UniProtKB:  P17787
PHAROS:  P17787
GTEx:  ENSG00000160716 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17787
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
J [auth C],
K [auth D],
M [auth E]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NCT
Query on NCT
Download Ideal Coordinates CCD File 
G [auth A],
L [auth D]		(S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE
C10 H14 N2
SNICXCGAKADSCV-JTQLQIEISA-N
NA
Query on NA
Download Ideal Coordinates CCD File 
H [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NCT BindingDB:  5KXI Ki: min: 0.05, max: 150 (nM) from 77 assay(s)
IC50: min: 1.2, max: 430 (nM) from 9 assay(s)
EC50: min: 1, max: 1.00e+4 (nM) from 25 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.94 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.285 
  • R-Value Observed: 0.286 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.099α = 90
b = 132.633β = 90
c = 202.44γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesT32 NS069562
Howard Hughes Medical Institute (HHMI)United StatesGilliam Fellowship
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesDA037492
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS077983
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS095899
Welch FoundationUnited StatesI-1812
McKnight Scholar AwardUnited States--
Klingenstein-Simons Fellowship AwardUnited States--
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesDA042072

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2016-10-19
    Changes: Database references
  • Version 1.2: 2016-11-02
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.6: 2024-04-03
    Changes: Data collection, Database references, Refinement description, Structure summary