Research workbench
An open-pore structure of a bacterial pentameric ligand- gated ion channel
Analyse An open-pore structure of a bacterial pentameric ligand- gated ion channel in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EAM
- Type
- protein
- Length
- 1,555 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GLR4197 protein
- UniProt
- Q7NDN8
- Ligands
- PC1
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | GLR4197 protein | protein | 311 | 39% helix, 33% strand | Q7NDN8 |
Ligands and binding sites
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 15 copies · chains A, E, B, C, D
- LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, B, E, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.81 | 0.82 | 65 | LMT |
| 2 | 416 | 0.73 | 0.83 | 51 | empty |
| 3 | 385 | 0.73 | 0.84 | 48 | empty |
| 4 | 372 | 0.73 | 0.84 | 48 | empty |
| 5 | 366 | 0.72 | 0.84 | 49 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2293 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 2285 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 2272 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 2259 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 2248 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3EAM · An open-pore structure of a bacterial pentameric ligand-gated ion channel · 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 D 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 Q7NDN8
- Elsewhere: RCSB PDB 3EAM · PDBe 3EAM · UniProt Q7NDN8
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