Research workbench
The active form of a pentameric ion channel (stelic) gated by alkaline pH - co-crystallization with 4-bromo cinnamic acid
Analyse The active form of a pentameric ion channel (stelic) gated by alkaline pH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FLI
- Type
- protein
- Length
- 1,550 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, DQZ
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Cys-loop ligand-gated ion channel | protein | 310 | 39% helix, 35% strand | G2FID1 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 5 copies · chains A, B, C, D, E
- DQZ · 3-(4-bromophenyl)propanoic acid · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.81 | 0.82 | 107 | DQZ |
| 2 | 774 | 0.79 | 0.82 | 71 | DQZ |
| 3 | 258 | 0.60 | 0.79 | 31 | empty |
| 4 | 246 | 0.59 | 0.79 | 30 | empty |
| 5 | 242 | 0.58 | 0.78 | 27 | empty |
Interfaces
10 interfaces between chains.
- B–C · 2406 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2406 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2400 Ų buried · 37 hydrogen bonds · protein-protein
- A–E · 2398 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 2386 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 6FLI · The active form of a pentameric ion channel (sTeLIC) gated by alkaline pH… · 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 6FLI · PDBe 6FLI · UniProt G2FID1
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