Research workbench
Cryo-EM structure of Xenopus tropicalis pannexin 1 channel
Analyse Cryo-EM structure of Xenopus tropicalis pannexin 1 channel in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VD7
- Type
- protein
- Length
- 2,079 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.02
- Source
- Xenopus tropicalis
- Molecule
- Pannexin
- UniProt
- B3DLA5
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · resolution 3.02 · 1 distinct chain · 62% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | Pannexin | protein | 297 | 62% helix, 4% strand | B3DLA5 |
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 | 857 | 0.81 | 0.83 | 87 | empty |
| 2 | 859 | 0.78 | 0.81 | 86 | empty |
| 3 | 840 | 0.78 | 0.81 | 93 | empty |
| 4 | 926 | 0.76 | 0.79 | 85 | empty |
| 5 | 1005 | 0.76 | 0.78 | 81 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2271 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 2269 Ų buried · 8 hydrogen bonds · protein-protein
- A–G · 2266 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 2265 Ų buried · 8 hydrogen bonds · protein-protein
- F–G · 2265 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 6VD7 · Cryo-EM structure of xenopus tropicalis pannexin 1 channel · the same entry in another collection · chain A against A, 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 B3DLA5
- Elsewhere: RCSB PDB 6VD7 · PDBe 6VD7 · UniProt B3DLA5
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