Research workbench
Cryo-EM structure of human pannexin 1 channel with deletion of N- terminal helix and C-terminal tail, in complex with cbx
Analyse Cryo-EM structure of human pannexin 1 channel with deletion of N- terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WBL
- Type
- protein
- Length
- 2,181 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pannexin-1
- UniProt
- Q96RD7
- Ligands
- CBO
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pannexin-1 | protein | 315 | 65% helix, 4% strand | Q96RD7 |
| C, F | Pannexin-1 | protein | 309 | 68% helix, 3% strand | Q96RD7 |
| D | Pannexin-1 | protein | 312 | 67% helix, 4% strand | Q96RD7 |
| E | Pannexin-1 | protein | 308 | 66% helix, 4% strand | Q96RD7 |
| G | Pannexin-1 | protein | 313 | 66% helix, 3% strand | Q96RD7 |
Ligands and binding sites
- CBO · Carbenoxolone · ligand · chains D, E, F
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 | 976 | 0.86 | 0.87 | 201 | empty |
| 2 | 766 | 0.84 | 0.87 | 145 | empty |
| 3 | 1152 | 0.83 | 0.84 | 191 | empty |
| 4 | 670 | 0.83 | 0.87 | 133 | empty |
| 5 | 733 | 0.81 | 0.85 | 123 | empty |
Interfaces
7 interfaces between chains.
- C–D · 841 Ų buried · 0 hydrogen bonds · protein-protein
- F–G · 829 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 796 Ų buried · 0 hydrogen bonds · protein-protein
- A–G · 779 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 682 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6WBL · Cryo-EM structure of human Pannexin 1 channel with deletion of N-terminal helix and… · the same entry in another collection · chain G against G, TM-score 1.00
- Q96RD7 · AlphaFold monomer V2.0 prediction for pannexin-1 (Q96RD7) · a predicted model of the same protein · chain C 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 Q96RD7
- Elsewhere: RCSB PDB 6WBL · PDBe 6WBL · UniProt Q96RD7
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