Research workbench
Structure of the pentameric ligand-gated ion channel elic in complex with a nam nanobody
Analyse Structure of the pentameric ligand-gated ion channel elic in complex with a nam… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SSP
- Type
- protein
- Length
- 3,260 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cys-loop ligand-gated ion channel; Nanobody 21
- UniProt
- P0C7B7
- Ligands
- UMQ, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 12 distinct chains · 32% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cys-loop ligand-gated ion channel | protein | 299 | 33% helix, 34% strand | P0C7B7 |
| B | Cys-loop ligand-gated ion channel | protein | 304 | 33% helix, 34% strand | P0C7B7 |
| C | Cys-loop ligand-gated ion channel | protein | 304 | 32% helix, 34% strand | P0C7B7 |
| D | Cys-loop ligand-gated ion channel | protein | 299 | 34% helix, 34% strand | P0C7B7 |
| E | Cys-loop ligand-gated ion channel | protein | 303 | 33% helix, 34% strand | P0C7B7 |
| F | Cys-loop ligand-gated ion channel | protein | 296 | 33% helix, 32% strand | P0C7B7 |
| G | Cys-loop ligand-gated ion channel | protein | 303 | 34% helix, 35% strand | P0C7B7 |
| H | Cys-loop ligand-gated ion channel | protein | 302 | 34% helix, 34% strand | P0C7B7 |
| I | Cys-loop ligand-gated ion channel | protein | 300 | 34% helix, 34% strand | P0C7B7 |
| J | Cys-loop ligand-gated ion channel | protein | 297 | 34% helix, 34% strand | P0C7B7 |
| K | Nanobody 21 | protein | 129 | 8% helix, 47% strand | — |
| L | Nanobody 21 | protein | 124 | 10% helix, 42% strand | — |
Ligands and binding sites
- UMQ · Undecyl-maltoside · ligand · 10 copies · chains A, E, B, C, D, F, J, G, H, I
- CA · Calcium ion · metal · 8 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 | 636 | 0.84 | 0.88 | 44 | empty |
| 2 | 658 | 0.83 | 0.87 | 48 | empty |
| 3 | 825 | 0.82 | 0.85 | 91 | CA |
| 4 | 862 | 0.81 | 0.83 | 98 | empty |
| 5 | 913 | 0.80 | 0.82 | 106 | CA |
Interfaces
28 interfaces between chains.
- B–C · 2579 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2555 Ų buried · 27 hydrogen bonds · protein-protein
- H–I · 2541 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 2502 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 2488 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6SSP · Structure of the pentameric ligand-gated ion channel ELIC in complex with a NAM nanobody · the same entry in another collection · chain L against L, 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 P0C7B7
- Elsewhere: RCSB PDB 6SSP · PDBe 6SSP · UniProt P0C7B7
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