Research workbench
Crystal structure of the ATP-gated human P2X3 ion channel in the ATP- bound, open state
Analyse Crystal structure of the ATP-gated human P2X3 ion channel in the ATP- bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SVK
- Type
- protein
- Length
- 714 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P2X purinoceptor 3
- UniProt
- P56373
- Ligands
- ATP, MHA, GLC, NAG
- Pockets
- 6 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | P2X purinoceptor 3 | protein | 357 | 29% helix, 36% strand | P56373 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MHA · (carbamoylmethyl-carboxymethyl-amino)-acetic acid · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.42 | 0.75 | 17 | empty |
| 2 | 86 | 0.35 | 0.75 | 15 | empty |
| 3 | 82 | 0.34 | 0.75 | 19 | empty |
| 4 | 62 | 0.33 | 0.76 | 18 | empty |
| 5 | 63 | 0.31 | 0.75 | 17 | empty |
Modifications
Observed in the structure: 10 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 5SVK · Crystal structure of the ATP-gated human P2X3 ion channel in the ATP-bound, open state · 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 5SVK · PDBe 5SVK · UniProt P56373
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