Research workbench
ELIC apo in POPC nanodisc
Analyse ELIC apo in POPC nanodisc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8D63
- Type
- protein
- Length
- 1,535 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.14
- Source
- Dickeya dadantii
- Molecule
- Erwinia ligand-gated ion channel
- UniProt
- E0SJQ4
- Ligands
- LBN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 3.14 · 1 distinct chain · 30% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Erwinia ligand-gated ion channel | protein | 307 | 30% helix, 32% strand | E0SJQ4 |
Ligands and binding sites
- LBN · 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine · ligand · 5 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.85 | 0.97 | 24 | empty |
| 2 | 785 | 0.79 | 0.83 | 79 | empty |
| 3 | 682 | 0.79 | 0.84 | 76 | empty |
| 4 | 775 | 0.79 | 0.83 | 81 | empty |
| 5 | 713 | 0.79 | 0.83 | 78 | empty |
Interfaces
10 interfaces between chains.
- A–E · 2613 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 2563 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 2545 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 2538 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 2514 Ų buried · 10 hydrogen bonds · protein-protein
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 E0SJQ4
- Elsewhere: RCSB PDB 8D63 · PDBe 8D63 · UniProt E0SJQ4
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