Research workbench
Cryo-EM structure of human pannexin 1 channel N255A mutant, gap junction
Analyse Cryo-EM structure of human pannexin 1 channel N255A mutant, gap junction in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WBN
- Type
- protein
- Length
- 4,774 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pannexin-1
- UniProt
- Q96RD7
- Ligands
- PTY, CLR, 3PE, DGA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 65% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N | Pannexin-1 | protein | 341 | 65% helix, 4% strand | Q96RD7 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 28 copies · chains A, B, G, C, D, E, F, H, I, N, J, K, L, M
- CLR · Cholesterol · ligand · 28 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 14 copies · chains A, G, B, C, D, E, F, H, N, I, J, K, L, M
- DGA · Diacyl glycerol · ligand · 14 copies · chains A, G, B, C, D, E, F, H, I, J, K, L, M, N
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 | 711 | 0.83 | 0.86 | 85 | DGA |
| 2 | 727 | 0.82 | 0.85 | 82 | DGA |
| 3 | 206 | 0.76 | 0.91 | 35 | empty |
| 4 | 193 | 0.74 | 0.90 | 29 | empty |
| 5 | 199 | 0.74 | 0.89 | 33 | empty |
Interfaces
21 interfaces between chains.
- M–N · 2338 Ų buried · 13 hydrogen bonds · protein-protein
- L–M · 2335 Ų buried · 13 hydrogen bonds · protein-protein
- J–K · 2332 Ų buried · 13 hydrogen bonds · protein-protein
- H–N · 2330 Ų buried · 13 hydrogen bonds · protein-protein
- H–I · 2327 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide (disulfide).
Compared structures
- 6WBN · Cryo-EM structure of human Pannexin 1 channel N255A mutant, gap junction · the same entry in another collection · chain N against N, 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 Q96RD7
- Elsewhere: RCSB PDB 6WBN · PDBe 6WBN · UniProt Q96RD7
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