Research workbench
Cryo-EM structure of human pannexin 1 channel with its C-terminal tail cleaved by caspase-7, in complex with cbx
Analyse Cryo-EM structure of human pannexin 1 channel with its C-terminal tail cleaved… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WBI
- Type
- protein
- Length
- 2,284 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 0.85
Structure
electron microscopy · 5 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pannexin-1 | protein | 323 | 66% helix, 4% strand | Q96RD7 |
| C | Pannexin-1 | protein | 327 | 67% helix, 4% strand | Q96RD7 |
| D | Pannexin-1 | protein | 325 | 65% helix, 3% strand | Q96RD7 |
| E, F | Pannexin-1 | protein | 329 | 68% helix, 4% strand | Q96RD7 |
| G | Pannexin-1 | protein | 328 | 67% helix, 4% strand | Q96RD7 |
Ligands and binding sites
- CBO · Carbenoxolone · ligand · chains A, B, E, F, G
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 | 767 | 0.85 | 0.88 | 136 | empty |
| 2 | 811 | 0.83 | 0.86 | 117 | empty |
| 3 | 531 | 0.83 | 0.89 | 103 | empty |
| 4 | 334 | 0.81 | 0.91 | 71 | empty |
| 5 | 356 | 0.81 | 0.90 | 71 | empty |
Interfaces
10 interfaces between chains.
- F–G · 1171 Ų buried · 2 hydrogen bonds · protein-protein
- A–G · 1118 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 1113 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 1092 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 1086 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6WBI · Cryo-EM structure of human Pannexin 1 channel with its C-terminal tail cleaved by… · 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 0.96
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 6WBI · PDBe 6WBI · UniProt Q96RD7
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