5SVR

Crystal structure of the ATP-gated human P2X3 ion channel bound to competitive antagonist A-317491

• PDB DOI: https://doi.org/10.2210/pdb5SVR/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2016-08-07 Released: 2016-10-05 
• Deposition Author(s): Mansoor, S.E., Lu, W., Oosterheert, W., Shekhar, M., Tajkhorshid, E., Gouaux, E.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.13 Å
• R-Value Free: 0.283 
• R-Value Work: 0.252 
• R-Value Observed: 0.254 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 41.8 kDa 
• Atom Count: 2,510 
• Modelled Residue Count: 327 
• Deposited Residue Count: 363 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P2X purinoceptor 3	A	363	Homo sapiens	Mutation(s): 3  Gene Names: P2RX3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P56373 (Homo sapiens) Explore P56373  Go to UniProtKB:  P56373
PHAROS:  P56373 GTEx:  ENSG00000109991

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
71C	F [auth A]	5-{[(3-phenoxyphenyl)methyl][(1S)-1,2,3,4-tetrahydronaphthalen-1-yl]carbamoyl}benzene-1,2,4-tricarboxylic acid C33 H27 N O8 VQGBOYBIENNKMI-LJAQVGFWSA-N
NAG	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
71C	BindingDB:  5SVR	Ki: min: 9, max: 10.8 (nM) from 2 assay(s)
		IC50: min: 35, max: 220 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.13 Å
• R-Value Free: 0.283 
• R-Value Work: 0.252 
• R-Value Observed: 0.254 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.17	α = 90
b = 123.17	β = 90
c = 237.46	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): Mansoor, S.E., Lu, W., Oosterheert, W., Shekhar, M., Tajkhorshid, E., Gouaux, E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5F32GM108391
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM100400

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2016-10-19
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary