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Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 3.1 ångströms

Analyse Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3H9V
Type: protein
Length: 329 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: P2X purinoceptor
UniProt: Q6NYR1
Ligands: NAG, GD
Pockets: 2 · best druggability 0.35

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	P2X purinoceptor	protein	329	20% helix, 38% strand	Q6NYR1

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
GD · Gadolinium atom · metal · 2 copies · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	82	0.35	0.75	22	empty
2	50	0.25	0.73	12	empty

Modifications

Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

3H9V · Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 3.1… · the same entry in another collection · chain A against A, TM-score 1.00

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 Q6NYR1
Elsewhere: RCSB PDB 3H9V · PDBe 3H9V · UniProt Q6NYR1

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