MolNFT v1 · #139981 · protein
Crystal structure of the chicken ATP-gated P2X7 receptor channel in the presence of competitive antagonist tnp-ATP at 3.1 ångströms
5XW6 · P2X purinoceptor: “Crystal structure of the chicken ATP-gated P2X7 receptor channel in the presence of competitive antagonist…”. X-ray diffraction, 2 ligands (128, NAG), 14 pockets (best druggability 0.87). MolNFT v1 #139981 on…
- PDB
- 5XW6
- Type
- protein
- Length
- 960 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P2X purinoceptor
- UniProt
- E1C6P3
- Ligands
- 128, NAG
- Pockets
- 14 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B | P2X purinoceptor | protein | 320 | 22% helix, 40% strand | E1C6P3 |
Ligands and binding sites
- 128 · Spiro(2,4,6-trinitrobenzene[1,2a]-2O',3O'-methylene-adenine-triphosphate · ligand · 3 copies · chains C, B, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.87 | 0.92 | 46 | empty |
| 2 | 659 | 0.79 | 0.84 | 67 | 128 |
| 3 | 551 | 0.76 | 0.83 | 60 | 128 |
| 4 | 652 | 0.76 | 0.82 | 64 | 128 |
| 5 | 713 | 0.69 | 0.77 | 57 | empty |
Interfaces
3 interfaces between chains.
- C–B · 2208 Ų buried · 26 hydrogen bonds · protein-protein
- C–A · 2204 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2176 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5XW6 · Crystal structure of the chicken ATP-gated P2X7 receptor channel in the presence of… · the same entry in another collection · chain C against C, 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 E1C6P3
- Elsewhere: RCSB PDB 5XW6 · PDBe 5XW6 · UniProt E1C6P3
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