Research workbench
X-ray structure of a pentameric ligand gated ion channel from erwinia chrysanthemi (elic) DELTA8 truncation mutant in complex with nanobody 72
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
- 6HJY
- Type
- protein
- Length
- 2,006 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cys-loop ligand-gated ion channel; Nanobody 72
- UniProt
- P0C7B7
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 26% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cys-loop ligand-gated ion channel | protein | 277 | 30% helix, 39% strand | P0C7B7 |
| B, C | Cys-loop ligand-gated ion channel | protein | 279 | 29% helix, 38% strand | P0C7B7 |
| D | Cys-loop ligand-gated ion channel | protein | 276 | 29% helix, 38% strand | P0C7B7 |
| E | Cys-loop ligand-gated ion channel | protein | 278 | 30% helix, 38% strand | P0C7B7 |
| F, J | Nanobody 72 | protein | 124 | 7% helix, 52% strand | — |
| G, H, I | Nanobody 72 | protein | 123 | 7% helix, 51% strand | — |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.86 | 0.89 | 117 | empty |
| 2 | 725 | 0.85 | 0.88 | 91 | empty |
| 3 | 967 | 0.84 | 0.86 | 135 | empty |
| 4 | 703 | 0.84 | 0.88 | 101 | empty |
| 5 | 962 | 0.83 | 0.84 | 118 | empty |
Interfaces
19 interfaces between chains.
- D–E · 2613 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 2604 Ų buried · 25 hydrogen bonds · protein-protein
- A–E · 2591 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2566 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2432 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6HJY · 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 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 P0C7B7
- Elsewhere: RCSB PDB 6HJY · PDBe 6HJY · UniProt P0C7B7
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