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Structure of human P2X3 receptor in complex with ATP and CA2+ ion

Analyse Structure of human P2X3 receptor in complex with ATP and CA2+ ion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AH4
Type: protein
Length: 1,071 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: P2X purinoceptor 3
UniProt: P56373
Ligands: ATP, GLC, NAG, CA
Pockets: 11 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	P2X purinoceptor 3	protein	357	27% helix, 38% strand	P56373

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, B, C
GLC · alpha-D-glucopyranose · sugar · 12 copies · chains A, C, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C
CA · Calcium ion · metal · 3 copies · chains A, B, C
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	883	0.87	0.89	81	empty
2	681	0.75	0.81	81	ATP, CA
3	705	0.70	0.77	72	ATP, CA
4	588	0.69	0.78	63	ATP, CA
5	902	0.67	0.74	73	empty

Interfaces

3 interfaces between chains.

B–C · 2782 Å² buried · 45 hydrogen bonds · protein-protein
A–C · 2768 Å² buried · 49 hydrogen bonds · protein-protein
A–B · 2672 Å² buried · 39 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 disulfide, 8 glycan, 7 covalent (disulfide, N-glycosylation, covalent ligand).

Compared structures

6AH4 · Structure of human P2X3 receptor in complex with ATP and Ca2+ ion · the same entry in another collection · chain A against A, TM-score 1.00
P56373 · AlphaFold monomer V2.0 prediction for P2X purinoceptor 3 (P56373) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P56373
Elsewhere: RCSB PDB 6AH4 · PDBe 6AH4 · UniProt P56373

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