Research workbench
Cardiac sodium channel with flecainide
Analyse Cardiac sodium channel with flecainide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UZ0
- Type
- protein
- Length
- 1,138 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium channel protein type 5 subunit ALPHA,GREEN fluorescent protein
- UniProt
- P15389, P42212
- Ligands
- 6OU, 9Z9, K4D, NAG, BMA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium channel protein type 5 subunit ALPHA,GREEN fluorescent protein | protein | 1138 | 70% helix, 1% strand | P15389, P42212 |
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
- 9Z9 · (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en · ligand · 5 copies · chains A
- K4D · Flecainide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- BMA · beta-D-mannopyranose · sugar
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 | 1014 | 0.87 | 0.87 | 75 | K4D |
| 2 | 496 | 0.71 | 0.81 | 63 | empty |
| 3 | 354 | 0.61 | 0.78 | 37 | empty |
| 4 | 328 | 0.61 | 0.78 | 50 | empty |
| 5 | 234 | 0.57 | 0.79 | 29 | empty |
Modifications
Observed in the structure: 5 glycan, 2 disulfide, 1 covalent (N-glycosylation, disulfide, covalent ligand, glycosylation).
Compared structures
- 6UZ0 · Cardiac sodium channel with flecainide · 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
- P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain A against A, TM-score 0.09
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 P42212
- Elsewhere: RCSB PDB 6UZ0 · PDBe 6UZ0 · UniProt P15389 · UniProt P42212
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