Research workbench
Cryo-EM structure of a human-cockroach hybrid nav channel bound to alpha-scorpion toxin AAH2.
Analyse Cryo-EM structure of a human-cockroach hybrid nav channel bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NT4
- Type
- protein
- Length
- 1,406 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium channel protein PAFPC1,SODIUM channel protein type 9 subunit ALPHA,SODIUM channel…
- UniProt
- D0E0C2, Q15858, P01484
- Ligands
- 76F, AJP, LHG, Y01, NAG, BMA, NH2
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 59% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium channel protein PAFPC1,SODIUM channel protein type 9 subunit ALPHA,SODIUM channel protein PAFPC1 | protein | 1278 | 61% helix, 1% strand | D0E0C2, Q15858 |
| B, C | Alpha-mammal toxin AAH2 | protein | 64 | 14% helix, 13% strand | P01484 |
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 · 5 copies · chains A
- AJP · Digitonin · ligand · chains A
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · chains A
- Y01 · Cholesterol hemisuccinate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, C
- NH2 · Amino group · ion · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 788 | 0.86 | 0.88 | 54 | empty |
| 2 | 500 | 0.80 | 0.87 | 58 | empty |
| 3 | 637 | 0.74 | 0.81 | 64 | NH2 |
| 4 | 934 | 0.72 | 0.76 | 66 | NAG, 76F |
| 5 | 615 | 0.69 | 0.78 | 60 | empty |
Interfaces
2 interfaces between chains.
- A–C · 774 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 456 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6NT4 · Cryo-EM structure of a human-cockroach hybrid Nav channel bound to alpha-scorpion toxin… · 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 0.94
- 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 0.91
- P01484 · AlphaFold monomer V2.0 prediction for alpha-mammal toxin AAH2 (P01484) · a predicted model of the same protein · chain B against A, TM-score 0.81
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
- Every structure of UniProt P01484
- Elsewhere: RCSB PDB 6NT4 · PDBe 6NT4 · UniProt D0E0C2 · UniProt Q15858 · UniProt P01484
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