Research workbench
X-ray structure of the pentameric ligand gated ion channel of gloebacter violaceus (glic) in a presumptive open conformation
Analyse X-ray structure of the pentameric ligand gated ion channel of gloebacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EHZ
- Type
- protein
- Length
- 1,550 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GLR4197 protein
- UniProt
- Q7NDN8
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | GLR4197 protein | protein | 310 | 35% helix, 32% strand | Q7NDN8 |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.79 | 0.80 | 62 | empty |
| 2 | 369 | 0.75 | 0.85 | 48 | empty |
| 3 | 373 | 0.73 | 0.84 | 52 | empty |
| 4 | 572 | 0.70 | 0.79 | 69 | empty |
| 5 | 342 | 0.69 | 0.82 | 44 | empty |
Interfaces
10 interfaces between chains.
- D–E · 2274 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 2255 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2246 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2234 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 2234 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3EHZ · X-ray structure of the pentameric ligand gated ion channel of Gloebacter violaceus (GLIC)… · the same entry in another collection · chain E against E, TM-score 1.00
- Q7NDN8 · AlphaFold monomer V2.0 prediction for proton-gated ion channel (Q7NDN8) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 Q7NDN8
- Elsewhere: RCSB PDB 3EHZ · PDBe 3EHZ · UniProt Q7NDN8
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