Research workbench
Voltage-gated sodium channel 1.5 (NAV1.5) C-terminal domain in complex with calmodulin poised for activation
Analyse Voltage-gated sodium channel 1.5 (NAV1.5) C-terminal domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OVN
- Type
- protein
- Length
- 1,458 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin; Sodium channel protein type 5 subunit alpha
- UniProt
- P62158, Q14524
- Ligands
- MG, SO4, PO4
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 7 distinct chains · 56% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Calmodulin | protein | 145 | 54% helix, 7% strand | P62158 |
| F | Sodium channel protein type 5 subunit alpha | protein | 146 | 53% helix, 9% strand | Q14524 |
| B, E | Calmodulin | protein | 144 | 50% helix, 7% strand | P62158 |
| G | Sodium channel protein type 5 subunit alpha | protein | 144 | 60% helix, 9% strand | Q14524 |
| H | Sodium channel protein type 5 subunit alpha | protein | 151 | 56% helix, 7% strand | Q14524 |
| I | Sodium channel protein type 5 subunit alpha | protein | 143 | 62% helix, 9% strand | Q14524 |
| J | Sodium channel protein type 5 subunit alpha | protein | 151 | 56% helix, 9% strand | Q14524 |
Ligands and binding sites
- MG · Magnesium ion · metal · 18 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 5 copies · chains A, F, G, C, H, E, J
- PO4 · Phosphate ion · ion · 2 copies · chains 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 746 | 0.72 | 0.78 | 69 | empty |
| 2 | 652 | 0.69 | 0.78 | 58 | empty |
| 3 | 687 | 0.69 | 0.77 | 64 | empty |
| 4 | 486 | 0.69 | 0.79 | 44 | empty |
| 5 | 540 | 0.67 | 0.77 | 39 | empty |
Interfaces
13 interfaces between chains.
- E–J · 1562 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 1521 Ų buried · 15 hydrogen bonds · protein-protein
- B–G · 1503 Ų buried · 18 hydrogen bonds · protein-protein
- C–H · 1474 Ų buried · 17 hydrogen bonds · protein-protein
- D–I · 1428 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 85 modified (engineered).
Compared structures
- 4OVN · Voltage-gated Sodium Channel 1.5 (Nav1.5) C-terminal domain in complex with Calmodulin… · the same entry in another collection · chain J against J, 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 H against A, TM-score 0.85
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 P62158
- Every structure of UniProt Q14524
- Elsewhere: RCSB PDB 4OVN · PDBe 4OVN · UniProt P62158 · UniProt Q14524
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