5SVJ
Crystal structure of the ATP-gated human P2X3 ion channel in the closed, apo state
- PDB DOI: https://doi.org/10.2210/pdb5SVJ/pdb
- Classification: MEMBRANE PROTEIN
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): Yes 
- Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc
- Deposited: 2016-08-06 Released: 2016-09-28 
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.98 Å
- R-Value Free: 0.259 
- R-Value Work: 0.212 
- R-Value Observed: 0.215 
This is version 1.4 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
P2X purinoceptor 3 | 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  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P56373 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | B [auth A], C [auth A], D [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
PG4 Query on PG4 | G [auth A] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N | |||
EDO Query on EDO | H [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N | |||
MG Query on MG | E [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N | |||
NA Query on NA | F [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.98 Å
- R-Value Free: 0.259 
- R-Value Work: 0.212 
- R-Value Observed: 0.215 
- Space Group: H 3 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 120.17 | α = 90 |
b = 120.17 | β = 90 |
c = 236.58 | γ = 120 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-09-28  Deposition Author(s): Mansoor, S.E., Lu, W., Oosterheert, W., Shekhar, M., Tajkhorshid, E., Gouaux, E.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | R01GM100400 |
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | 5F32GM108391 |
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: 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