Research workbench
Structure of the pentameric ligand-gated ion channel ELIC in complex with a PAM nanobody
Analyse Structure of the pentameric ligand-gated ion channel ELIC in complex with a PAM… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SSI
- Type
- protein
- Length
- 2,081 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.59
- Source
- Dickeya chrysanthemi; Lama glama
- Molecule
- Cys-loop ligand-gated ion channel; Nanobody 22
- UniProt
- P0C7B7
- Ligands
- ABU, UMQ, CA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.59 · 8 distinct chains · 27% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cys-loop ligand-gated ion channel | protein | 303 | 33% helix, 34% strand | P0C7B7 |
| B | Cys-loop ligand-gated ion channel | protein | 308 | 32% helix, 33% strand | P0C7B7 |
| C | Cys-loop ligand-gated ion channel | protein | 307 | 32% helix, 33% strand | P0C7B7 |
| D | Cys-loop ligand-gated ion channel | protein | 305 | 32% helix, 35% strand | P0C7B7 |
| E | Cys-loop ligand-gated ion channel | protein | 304 | 32% helix, 34% strand | P0C7B7 |
| F, J | Nanobody 22 | protein | 110 | 5% helix, 60% strand | — |
| G, I | Nanobody 22 | protein | 111 | 3% helix, 59% strand | — |
| H | Nanobody 22 | protein | 112 | 3% helix, 58% strand | — |
Ligands and binding sites
- ABU · Gamma-amino-butanoic acid · ligand · 5 copies · chains A, B, C, D, E
- UMQ · Undecyl-maltoside · ligand · 5 copies · chains A, B, C, D, E
- CA · Calcium ion · metal · 5 copies · chains A, E, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, E, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 5 copies · chains A, B, C, D, E
- PG4 · Tetraethylene glycol · additive · 4 copies · chains B, C, D, E
- ACT · Acetate ion · additive · 2 copies · chains C, D, E
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 | 201 | 0.83 | 0.96 | 21 | empty |
| 2 | 897 | 0.83 | 0.85 | 104 | ABU, GOL, CA |
| 3 | 849 | 0.83 | 0.85 | 91 | ABU, GOL, CA |
| 4 | 969 | 0.82 | 0.83 | 100 | ABU, GOL, CA |
| 5 | 1009 | 0.81 | 0.82 | 105 | GOL, CA, ABU, MES |
Interfaces
20 interfaces between chains.
- D–E · 2467 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 2466 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 2436 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2379 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2376 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6SSI · Structure of the pentameric ligand-gated ion channel elic in complex with a pam nanobody · 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 A 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 6SSI · PDBe 6SSI · UniProt P0C7B7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.