Research workbench
Crystal structure of human NAV1.4 cterminal domain in complex with apo calmodulin
Analyse Crystal structure of human NAV1.4 cterminal domain in complex with apo… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MBA
- Type
- protein
- Length
- 275 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium channel protein type 4 subunit alpha; Calmodulin-1
- UniProt
- P35499, P0DP29
- Ligands
- CL, CO3
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium channel protein type 4 subunit alpha | protein | 130 | 63% helix, 8% strand | P35499 |
| B | Calmodulin-1 | protein | 145 | 58% helix, 8% strand | P0DP29 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B
- CO3 · Carbonate ion · ion · chains B
- EDO · 1,2-ethanediol · additive · chains B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.70 | 0.80 | 61 | empty |
| 2 | 64 | 0.33 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1582 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 6MBA · Crystal Structure of Human Nav1.4 CTerminal Domain in Complex with apo Calmodulin · the same entry in another collection · chain A against A, TM-score 1.00
- P35499 · AlphaFold monomer V2.0 prediction for sodium channel protein type 4 subunit alpha (P35499) · a predicted model of the same protein · chain A against A, TM-score 0.82
- P0DP29 · AlphaFold monomer V2.0 prediction for calmodulin-1 (P0DP29) · a predicted model of the same protein · chain B against A, TM-score 0.42
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 P35499
- Every structure of UniProt P0DP29
- Elsewhere: RCSB PDB 6MBA · PDBe 6MBA · UniProt P35499 · UniProt P0DP29
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