Research workbench
Anomalous MN2+ signal reveals a divalent cation-binding site in the head domain of the ATP-gated human P2X3 ion channel
Analyse Anomalous MN2+ signal reveals a divalent cation-binding site in the head domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SVS
- Type
- protein
- Length
- 322 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P2X purinoceptor 3
- UniProt
- P56373
- Ligands
- NAG, MG, NA
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P2X purinoceptor 3 | protein | 322 | 26% helix, 39% strand | P56373 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- EDO · 1,2-ethanediol · additive · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.34 | 0.75 | 15 | empty |
| 2 | 80 | 0.32 | 0.74 | 17 | MG |
Modifications
Observed in the structure: 5 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5SVS · Anomalous Mn2+ signal reveals a divalent cation-binding site in the head domain of the… · 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 0.92
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 5SVS · PDBe 5SVS · UniProt P56373
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