Research workbench
Structure of NAVAB/NAV1.7-VS2A chimera trapped in the resting state by tarantula toxin M3-huwentoxin-IV
Analyse Structure of NAVAB/NAV1.7-VS2A chimera trapped in the resting state by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K48
- Type
- protein
- Length
- 1,048 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,ION transport PROTEIN,SODIUM channel…
- UniProt
- A8EVM5, Q15858, P83303
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 2 distinct chains · 72% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,ION transport PROTEIN,SODIUM channel protein type 9 subunit alpha chimera | protein | 229 | 81% helix, 0% strand | A8EVM5, Q15858 |
| E, F, G, H | Mu-theraphotoxin-HS2A | protein | 33 | 9% helix, 24% strand | P83303 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.88 | 0.88 | 105 | empty |
| 2 | 407 | 0.72 | 0.83 | 54 | empty |
| 3 | 357 | 0.72 | 0.84 | 44 | empty |
| 4 | 391 | 0.72 | 0.83 | 47 | empty |
| 5 | 368 | 0.71 | 0.83 | 47 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1840 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 1817 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1794 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 1786 Ų buried · 5 hydrogen bonds · protein-protein
- C–G · 491 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7K48 · Structure of NavAb/Nav1.7-VS2A chimera trapped in the resting state by tarantula toxin… · the same entry in another collection · chain H against H, TM-score 1.00
- Q15858 · AlphaFold monomer V2.0 prediction for sodium channel protein type 9 subunit alpha (Q15858) · a predicted model of the same protein · chain C against A, TM-score 0.87
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 A8EVM5
- Every structure of UniProt Q15858
- Every structure of UniProt P83303
- Elsewhere: RCSB PDB 7K48 · PDBe 7K48 · UniProt A8EVM5 · UniProt Q15858 · UniProt P83303
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