MolNFT v1 · #157289 · protein
Voltage-gated sodium channel NAV1.5 C-terminal domain in complex with CA2+/CALMODULIN
6MUD · Calmodulin-1: “Voltage-gated sodium channel NAV1.5 C-terminal domain in complex with CA2+/CALMODULIN”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.63). MolNFT v1 #157289 on GenesisL1: 3D structure, binding sites…
- PDB
- 6MUD
- Type
- protein
- Length
- 275 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin-1; Sodium channel protein type 5 subunit alpha
- UniProt
- P0DP23, Q14524
- Ligands
- CA
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calmodulin-1 | protein | 147 | 59% helix, 4% strand | P0DP23 |
| B | Sodium channel protein type 5 subunit alpha | protein | 128 | 61% helix, 8% strand | Q14524 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.63 | 0.86 | 24 | empty |
| 2 | 417 | 0.57 | 0.74 | 40 | empty |
| 3 | 50 | 0.35 | 0.78 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 752 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6MUD · Voltage-gated sodium channel NaV1.5 C-terminal domain in complex with Ca2+/Calmodulin · the same entry in another collection · chain A against A, TM-score 1.00
- Q14524 · AlphaFold monomer V2.0 prediction for sodium channel protein type 5 subunit alpha (Q14524) · a predicted model of the same protein · chain B against A, TM-score 0.91
- P0DP23 · AlphaFold monomer V2.0 prediction for calmodulin-1 (P0DP23) · a predicted model of the same protein · chain A against A, TM-score 0.54
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 P0DP23
- Every structure of UniProt Q14524
- Elsewhere: RCSB PDB 6MUD · PDBe 6MUD · UniProt P0DP23 · UniProt Q14524
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