MolNFT v1 · #159972 · protein
Cryo-EM structure of voltage-gated sodium channel navab N49K/L109A/M116V/G94C/Q150C disulfide crosslinked mutant in the resting state
6P6W · Fusion of maltose-binding protein and voltage-gated sodium…: “Cryo-EM structure of voltage-gated sodium channel navab N49K/L109A/M116V/G94C/Q150C disulfide crosslinked…”. Electron microscopy, 20 pockets (best druggability 0.86).…
- PDB
- 6P6W
- Type
- protein
- Length
- 916 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion of maltose-binding protein and voltage-gated sodium channel navab
- UniProt
- A0A028ANC5, A8EVM5
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fusion of maltose-binding protein and voltage-gated sodium channel navab | protein | 229 | 76% helix, 0% strand | A0A028ANC5, A8EVM5 |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.86 | 0.86 | 77 | empty |
| 2 | 512 | 0.66 | 0.77 | 55 | empty |
| 3 | 277 | 0.65 | 0.81 | 34 | empty |
| 4 | 365 | 0.64 | 0.78 | 34 | empty |
| 5 | 355 | 0.63 | 0.78 | 33 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2022 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 2013 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 2000 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1997 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 55 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6P6W · Cryo-EM structure of voltage-gated sodium channel NavAb N49K/L109A/M116V/G94C/Q150C… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A028ANC5
- Every structure of UniProt A8EVM5
- Elsewhere: RCSB PDB 6P6W · PDBe 6P6W · UniProt A0A028ANC5 · UniProt A8EVM5
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