Research workbench
X-ray structure of a pentameric ligand gated ion channel from erwinia chrysanthemi (elic) in complex with zopiclone
Analyse X-ray structure of a pentameric ligand gated ion channel from erwinia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A97
- Type
- protein
- Length
- 3,070 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cys-loop ligand-gated ion channel
- UniProt
- P0C7B7
- Ligands
- ZPC
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Cys-loop ligand-gated ion channel | protein | 307 | 32% helix, 34% strand | P0C7B7 |
Ligands and binding sites
- ZPC · (5R)-6-(5-chloropyridin-2-yl)-7-oxo-6,7-dihydro-5H-pyrrolo[3,4-b]pyrazin-5-yl 4-methylpiperazine-1-carboxylate · ligand · 10 copies · chains A, E, B, C, D, F, J, G, H, I
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 | 984 | 0.83 | 0.84 | 104 | ZPC |
| 2 | 901 | 0.83 | 0.85 | 94 | ZPC |
| 3 | 1072 | 0.83 | 0.84 | 104 | ZPC |
| 4 | 965 | 0.83 | 0.84 | 100 | ZPC |
| 5 | 1065 | 0.82 | 0.83 | 98 | ZPC |
Interfaces
20 interfaces between chains.
- A–E · 2706 Ų buried · 20 hydrogen bonds · protein-protein
- F–J · 2699 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 2663 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2662 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 2658 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4A97 · X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC)… · the same entry in another collection · chain J against J, TM-score 1.00
- P0C7B7 · AlphaFold monomer V2.0 prediction for cys-loop ligand-gated ion channel (P0C7B7) · a predicted model of the same protein · chain J against A, TM-score 0.98
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 P0C7B7
- Elsewhere: RCSB PDB 4A97 · PDBe 4A97 · UniProt P0C7B7
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