Research workbench
X-ray structure of a pentameric ligand gated ion channel from erwinia chrysanthemi (elic) 7'C pore mutant (L238C) 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
- 6HJX
- Type
- protein
- Length
- 2,131 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
- Ligands
- PTY, NA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 9 distinct chains · 27% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cys-loop ligand-gated ion channel | protein | 303 | 35% helix, 34% strand | P0C7B7 |
| B | Cys-loop ligand-gated ion channel | protein | 309 | 32% helix, 35% strand | P0C7B7 |
| C | Cys-loop ligand-gated ion channel | protein | 305 | 32% helix, 35% strand | P0C7B7 |
| D | Cys-loop ligand-gated ion channel | protein | 302 | 33% helix, 36% strand | P0C7B7 |
| E | Cys-loop ligand-gated ion channel | protein | 299 | 34% helix, 35% strand | P0C7B7 |
| F, J | Nanobody 72 | protein | 124 | 10% helix, 52% strand | — |
| G | Nanobody 72 | protein | 122 | 7% helix, 50% strand | — |
| H | Nanobody 72 | protein | 122 | 7% helix, 51% strand | — |
| I | Nanobody 72 | protein | 121 | 7% helix, 49% strand | — |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · chains A, B
- NA · Sodium ion · metal · chains C, D
- LMT · Dodecyl-beta-D-maltoside · additive · 5 copies · chains A, E, B, C, D
- P6G · Hexaethylene glycol · additive · 4 copies · chains A, B, D, E
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B, C
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 | 857 | 0.86 | 0.88 | 123 | MES |
| 2 | 1115 | 0.86 | 0.86 | 139 | empty |
| 3 | 982 | 0.86 | 0.87 | 126 | empty |
| 4 | 1049 | 0.85 | 0.86 | 126 | empty |
| 5 | 690 | 0.83 | 0.87 | 91 | empty |
Interfaces
20 interfaces between chains.
- D–E · 2570 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2557 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 2424 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 2382 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2375 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6HJX · 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 0.98
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 6HJX · PDBe 6HJX · UniProt P0C7B7
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