Research workbench
Cryoem structure of NAV1.7 VSD2 (deactived state) in complex with the gating modifier toxin PROTX2
Analyse Cryoem structure of NAV1.7 VSD2 (deactived state) in complex with the gating… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N4R
- Type
- protein
- Length
- 1,942 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAV1.7 VSD2-navab chimera; BETA/OMEGA-theraphotoxin-TP2A; Fab light chain; Fab heavy chain
- UniProt
- A8EVM5, Q15858, P83476
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | NAV1.7 VSD2-navab chimera | protein | 225 | 74% helix, 0% strand | A8EVM5, Q15858 |
| C, A | NAV1.7 VSD2-navab chimera | protein | 243 | 76% helix, 0% strand | A8EVM5, Q15858 |
| E, F, G, H | BETA/OMEGA-theraphotoxin-TP2A | protein | 30 | 0% helix, 33% strand | P83476 |
| I, K | Fab light chain | protein | 215 | 5% helix, 47% strand | — |
| J, L | Fab heavy chain | protein | 228 | 4% helix, 50% strand | — |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.85 | 0.86 | 85 | empty |
| 2 | 718 | 0.73 | 0.79 | 71 | empty |
| 3 | 793 | 0.73 | 0.78 | 66 | empty |
| 4 | 377 | 0.66 | 0.79 | 45 | empty |
| 5 | 288 | 0.63 | 0.80 | 33 | empty |
Interfaces
24 interfaces between chains.
- I–J · 1884 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1864 Ų buried · 5 hydrogen bonds · protein-protein
- D–A · 1852 Ų buried · 5 hydrogen bonds · protein-protein
- K–L · 1842 Ų buried · 10 hydrogen bonds · protein-protein
- B–A · 1697 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide (disulfide).
Compared structures
- 6N4R · CryoEM structure of Nav1.7 VSD2 (deactived state) in complex with the gating modifier… · 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 A8EVM5
- Every structure of UniProt Q15858
- Every structure of UniProt P83476
- Elsewhere: RCSB PDB 6N4R · PDBe 6N4R · UniProt A8EVM5 · UniProt Q15858 · UniProt P83476
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