9OMR | pdb_00009omr

The desensitized state structure of human P2X2 receptor channel in lipid nanodiscs with free ATP and sodium

PDB DOI: https://doi.org/10.2210/pdb9OMR/pdb
EM Map EMD-70617: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-05-14 Released: 2026-03-18
Deposition Author(s): Dhingra, S., Swartz, K.J.
Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.68 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

The desensitized state structure of human P2X2 receptor channel in lipid nanodiscs with free ATP and sodium

Dhingra, S., Swartz, K.J.

To be published.

Macromolecule Content

Total Structure Weight: 158.96 kDa
Atom Count: 7,584
Modeled Residue Count: 945
Deposited Residue Count: 1,413
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P2X purinoceptor 2	A, B, C	471	Homo sapiens	Mutation(s): 0 Gene Names: P2RX2, P2X2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBL9 (Homo sapiens) Explore Q9UBL9 Go to UniProtKB: Q9UBL9
PHAROS: Q9UBL9 GTEx: ENSG00000187848
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UBL9
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: Q9UBL9-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B], O [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain J [auth B] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] H [auth B] I [auth B] D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], L [auth C], M [auth C], N [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C]