MolNFT v1 · #118421 · protein
Crystal structure of an invertebrate P2X receptor from the gulf coast tick in the presence of ATP and ZN2+ ion at 2.9 ångströms
5F1C · Putative uncharacterized protein: “Crystal structure of an invertebrate P2X receptor from the gulf coast tick in the presence of ATP and ZN2+…”. X-ray diffraction, 3 ligands (ATP, NAG, ZN), 10 pockets (best druggability 0.87).…
- PDB
- 5F1C
- Type
- protein
- Length
- 1,042 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- G3MM57
- Ligands
- ATP, NAG, ZN
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein | protein | 343 | 21% helix, 36% strand | G3MM57 |
| B | Putative uncharacterized protein | protein | 355 | 22% helix, 35% strand | G3MM57 |
| C | Putative uncharacterized protein | protein | 344 | 22% helix, 36% strand | G3MM57 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, C, B
- ZN · Zinc ion · metal · 13 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.87 | 0.90 | 68 | empty |
| 2 | 434 | 0.80 | 0.88 | 70 | ZN, ATP |
| 3 | 476 | 0.80 | 0.87 | 89 | ZN, ATP |
| 4 | 410 | 0.79 | 0.88 | 66 | ATP, ZN |
| 5 | 232 | 0.57 | 0.79 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1818 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1794 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1770 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5F1C · Crystal structure of an invertebrate P2X receptor from the Gulf Coast tick in the… · 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 G3MM57
- Elsewhere: RCSB PDB 5F1C · PDBe 5F1C · UniProt G3MM57
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