MolNFT v1 · #168292 · protein
Cryo-EM structure of human pannexin 1 channel with its C-terminal tail cleaved by caspase-7
6WBG · Pannexin-1: “Cryo-EM structure of human pannexin 1 channel with its C-terminal tail cleaved by caspase-7”. Electron microscopy, 5 ligands (PTY, CLR, 3PE), 20 pockets (best druggability 0.78). MolNFT v1 #168292 on GenesisL1: 3D…
- PDB
- 6WBG
- Type
- protein
- Length
- 2,408 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pannexin-1
- UniProt
- Q96RD7
- Ligands
- PTY, CLR, 3PE, DGA, NAG
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 1 distinct chain · 63% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | Pannexin-1 | protein | 344 | 63% helix, 4% strand | Q96RD7 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 14 copies · chains A, B, G, C, D, E, F
- CLR · Cholesterol · ligand · 14 copies · chains A, B, C, D, E, F, G
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 7 copies · chains A, G, B, C, D, E, F
- DGA · Diacyl glycerol · ligand · 7 copies · chains A, G, B, C, D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B, C, D, 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 | 398 | 0.78 | 0.87 | 63 | empty |
| 2 | 311 | 0.76 | 0.87 | 53 | DGA |
| 3 | 316 | 0.76 | 0.87 | 53 | DGA |
| 4 | 278 | 0.73 | 0.85 | 33 | DGA |
| 5 | 340 | 0.72 | 0.83 | 34 | DGA |
Interfaces
7 interfaces between chains.
- A–G · 2397 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 2397 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 2395 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 2392 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2390 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 6WBG · 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 A 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 6WBG · PDBe 6WBG · UniProt Q96RD7
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