Research workbench
The active form of a pentameric ion channel (stelic) gated by alkaline pH - R86A
Analyse The active form of a pentameric ion channel (stelic) gated by alkaline pH - R86A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FVQ
- Type
- protein
- Length
- 1,545 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cys-loop ligand-gated ion channel
- UniProt
- G2FID1
- Ligands
- BNG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Cys-loop ligand-gated ion channel | protein | 309 | 38% helix, 36% strand | G2FID1 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 5 copies · chains A, E, B, C, D
- PG4 · Tetraethylene glycol · additive · 5 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.80 | 0.83 | 72 | PG4 |
| 2 | 693 | 0.80 | 0.84 | 73 | PG4 |
| 3 | 368 | 0.71 | 0.82 | 40 | PG4 |
| 4 | 277 | 0.58 | 0.77 | 32 | empty |
| 5 | 246 | 0.58 | 0.78 | 29 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2449 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2434 Ų buried · 40 hydrogen bonds · protein-protein
- A–E · 2423 Ų buried · 39 hydrogen bonds · protein-protein
- D–E · 2415 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2411 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 6FVQ · The active form of a pentameric ion channel (sTeLIC) gated by alkaline pH - R86A · 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 G2FID1
- Elsewhere: RCSB PDB 6FVQ · PDBe 6FVQ · UniProt G2FID1
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