Research workbench
Cryo-EM structure of a human-cockroach hybrid nav channel.
Analyse Cryo-EM structure of a human-cockroach hybrid nav channel. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NT3
- Type
- protein
- Length
- 1,278 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium channel protein type 9 subunit alpha, sodium channel protein PAFPC1, chimeric…
- UniProt
- D0E0C2, Q15858
- Ligands
- 76F, Y01, LHG, AJP, NAG, BMA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 58% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium channel protein type 9 subunit alpha, sodium channel protein PAFPC1, chimeric construct | protein | 1278 | 58% helix, 2% strand | D0E0C2, Q15858 |
Ligands and binding sites
- 76F · (7E,21R,24S)-27-amino-24-hydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaheptacos-7-en-21-yl (9Z, 12E)-octadeca-9,12-dienoate · ligand · 4 copies · chains A
- Y01 · Cholesterol hemisuccinate · ligand · chains A
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · chains A
- AJP · Digitonin · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.85 | 0.85 | 88 | empty |
| 2 | 667 | 0.68 | 0.76 | 57 | empty |
| 3 | 423 | 0.66 | 0.79 | 42 | empty |
| 4 | 299 | 0.65 | 0.81 | 33 | empty |
| 5 | 375 | 0.63 | 0.78 | 39 | empty |
Modifications
Observed in the structure: 6 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 6NT3 · Cryo-EM structure of a human-cockroach hybrid Nav channel. · the same entry in another collection · chain A against A, TM-score 1.00
- D0E0C2 · AlphaFold monomer V2.0 prediction for sodium channel protein PAFPC1 (D0E0C2) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q15858 · AlphaFold monomer V2.0 prediction for sodium channel protein type 9 subunit alpha (Q15858) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 D0E0C2
- Every structure of UniProt Q15858
- Elsewhere: RCSB PDB 6NT3 · PDBe 6NT3 · UniProt D0E0C2 · UniProt Q15858
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