MolNFT v1 · #179297 · protein
Cardiac sodium channel with toxin bound
7K18 · Sodium channel protein type 5 subunit alpha, enhanced green…: “Cardiac sodium channel with toxin bound”. Electron microscopy, 3 ligands (6OU, NAG, BMA), 19 pockets (best druggability 0.86). MolNFT v1 #179297 on GenesisL1: 3D…
- PDB
- 7K18
- Type
- protein
- Length
- 1,195 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium channel protein type 5 subunit alpha, enhanced green fluorescent protein…
- UniProt
- P15389, P56678
- Ligands
- 6OU, NAG, BMA
- Pockets
- 19 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium channel protein type 5 subunit alpha, enhanced green fluorescent protein | protein | 1128 | 69% helix, 1% strand | P15389 |
| B | Alpha-like toxin LQH3 | protein | 67 | 10% helix, 27% strand | P56678 |
Ligands and binding sites
- 6OU · [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate · ligand · 11 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.86 | 0.86 | 88 | empty |
| 2 | 812 | 0.75 | 0.80 | 74 | empty |
| 3 | 527 | 0.70 | 0.80 | 63 | empty |
| 4 | 517 | 0.66 | 0.77 | 44 | empty |
| 5 | 263 | 0.65 | 0.82 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 432 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 7K18 · Cardiac Sodium channel with toxin bound · the same entry in another collection · chain A against A, TM-score 1.00
- P15389 · AlphaFold monomer V2.0 prediction for sodium channel protein type 5 subunit alpha (P15389) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P56678 · AlphaFold monomer V2.0 prediction for alpha-like toxin LQH3 (P56678) · 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 P15389
- Every structure of UniProt P56678
- Elsewhere: RCSB PDB 7K18 · PDBe 7K18 · UniProt P15389 · UniProt P56678
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