Research workbench
Anomalous sulfur signal reveals the position of agonist 2-methylthio- ATP bound to the ATP-gated human P2X3 ion channel in the desensitized state
Analyse Anomalous sulfur signal reveals the position of agonist 2-methylthio- ATP bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SVP
- Type
- protein
- Length
- 643 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P2X purinoceptor 3
- UniProt
- P56373
- Ligands
- 6AT, ATP, NAG, NA
- Pockets
- 4 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P2X purinoceptor 3 | protein | 323 | 28% helix, 41% strand | P56373 |
| B | P2X purinoceptor 3 | protein | 320 | 27% helix, 40% strand | P56373 |
Ligands and binding sites
- 6AT · 2-(methylsulfanyl)adenosine 5'-(tetrahydrogen triphosphate) · ligand · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 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 | 0.36 | 0.76 | 16 | empty |
| 2 | 55 | 0.33 | 0.77 | 15 | empty |
| 3 | 62 | 0.32 | 0.76 | 13 | empty |
| 4 | 52 | 0.30 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 31 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- P56373 · AlphaFold monomer V2.0 prediction for P2X purinoceptor 3 (P56373) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 5SVP · PDBe 5SVP · UniProt P56373
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.