Research workbench
Cryo-EM structure of the ZAC zinc-activated channel in the Cys-loop receptor superfamily
Analyse Cryo-EM structure of the ZAC zinc-activated channel in the Cys-loop receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8WGE
- Type
- protein
- Length
- 1,740 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.4
- Source
- Oryzias latipes
- Molecule
- Zac
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 3.4 · 1 distinct chain · 40% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Zac | protein | 348 | 40% helix, 27% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.83 | 0.84 | 125 | empty |
| 2 | 417 | 0.70 | 0.80 | 38 | empty |
| 3 | 535 | 0.66 | 0.77 | 77 | empty |
| 4 | 341 | 0.60 | 0.78 | 46 | empty |
| 5 | 327 | 0.59 | 0.78 | 53 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2831 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 2823 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2820 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 2814 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 2805 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 5 glycan (disulfide, N-glycosylation).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 8WGE · PDBe 8WGE
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