8JV7

Cryo-EM structure of the panda P2X7 receptor in complex with PPADS

PDB DOI: https://doi.org/10.2210/pdb8JV7/pdb
EM Map EMD-36670: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Ailuropoda melanoleuca
Expression System: Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2023-06-27 Released: 2023-11-29
Deposition Author(s): Sheng, D., Hattori, M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural insights into the orthosteric inhibition of P2X receptors by non-ATP-analog antagonists

Sheng, D., Yue, C., Jin, F., Wang, Y., Ichikawa, M., Yu, Y., Guo, C.R., Hattori, M.

(2023) Elife

DOI: https://doi.org/10.7554/eLife.92829.1

Macromolecule Content

Total Structure Weight: 119.01 kDa
Atom Count: 7,245
Modelled Residue Count: 960
Deposited Residue Count: 1,026
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	A, B, C	342	Ailuropoda melanoleuca	Mutation(s): 5 Gene Names: PANDA_000894 Membrane Entity: Yes
UniProt
Find proteins for G1M6C4 (Ailuropoda melanoleuca) Explore G1M6C4 Go to UniProtKB: G1M6C4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G1M6C4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UO6 (Subject of Investigation/LOI) Query on UO6 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C]	F [auth A], I [auth B], L [auth C]	4-[(E)-[4-methanoyl-6-methyl-5-oxidanyl-3-(phosphonooxymethyl)pyridin-2-yl]diazenyl]benzene-1,3-disulfonic acid C₁₄ H₁₄ N₃ O₁₂ P S₂ PNFZSRRRZNXSMF-WUKNDPDISA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C]	D [auth A] E [auth A] G [auth B] H [auth B] J [auth C] D [auth A], E [auth A], G [auth B], H [auth B], J [auth C], K [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 G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C]