Research workbench
Cryo-EM structure of the C-terminal deletion mutant of human PANX1 in a nanodisc
Analyse Cryo-EM structure of the C-terminal deletion mutant of human PANX1 in a nanodisc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F8O
- Type
- protein
- Length
- 2,184 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pannexin-1
- UniProt
- Q96RD7
- Ligands
- LBN
- Pockets
- 20 · best druggability 0.79
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 | 312 | 63% helix, 4% strand | Q96RD7 |
Ligands and binding sites
- LBN · 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine · ligand · 21 copies · chains A, B, G, C, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.79 | 0.80 | 112 | empty |
| 2 | 907 | 0.78 | 0.80 | 91 | LBN |
| 3 | 810 | 0.77 | 0.80 | 86 | empty |
| 4 | 830 | 0.76 | 0.80 | 82 | empty |
| 5 | 795 | 0.76 | 0.80 | 83 | LBN |
Interfaces
7 interfaces between chains.
- F–G · 2516 Ų buried · 23 hydrogen bonds · protein-protein
- A–G · 2495 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 2490 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 2486 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2449 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 7F8O · Cryo-EM structure of the C-terminal deletion mutant of human PANX1 in a nanodisc · 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 7F8O · PDBe 7F8O · UniProt Q96RD7
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