MolNFT v1 · #142588 · protein
Complex of voltage-gated sodium channel navpas from american cockroach periplaneta americana and DC1A
6A90 · Sodium channel protein PAFPC1: “Complex of voltage-gated sodium channel navpas from american cockroach periplaneta americana and DC1A”. Electron microscopy, 2 ligands (NAG, NA), 20 pockets (best druggability 0.85). MolNFT v1 #142588…
- PDB
- 6A90
- Type
- protein
- Length
- 1,380 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium channel protein PAFPC1; Mu-diguetoxin-DC1A
- UniProt
- D0E0C2, P49126
- Ligands
- NAG, NA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 61% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium channel protein PAFPC1 | protein | 1323 | 64% helix, 2% strand | D0E0C2 |
| B | Mu-diguetoxin-DC1A | protein | 57 | 0% helix, 42% strand | P49126 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- NA · Sodium ion · metal · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.85 | 0.86 | 84 | empty |
| 2 | 663 | 0.68 | 0.76 | 57 | empty |
| 3 | 457 | 0.66 | 0.78 | 40 | empty |
| 4 | 205 | 0.64 | 0.83 | 23 | empty |
| 5 | 286 | 0.60 | 0.78 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 1183 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6A90 · Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta… · the same entry in another collection · chain A against A, TM-score 1.00
- P49126 · AlphaFold monomer V2.0 prediction for beta-diguetoxin-DC1A (P49126) · a predicted model of the same protein · chain B against A, TM-score 0.94
- 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 0.92
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 P49126
- Elsewhere: RCSB PDB 6A90 · PDBe 6A90 · UniProt D0E0C2 · UniProt P49126
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