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Structural basis of NAV1.7 inhibition by a gating-modifier spider toxin
Analyse Structural basis of NAV1.7 inhibition by a gating-modifier spider toxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N4I
- Type
- protein
- Length
- 1,021 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAV1.7 VSD2-navab channel chimera protein; BETA/OMEGA-theraphotoxin-TP2A
- UniProt
- P83476
- Ligands
- 6OU
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 78% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | NAV1.7 VSD2-navab channel chimera protein | protein | 225 | 83% helix, 0% strand | — |
| C | NAV1.7 VSD2-navab channel chimera protein | protein | 226 | 84% helix, 0% strand | — |
| E, F, G, H | BETA/OMEGA-theraphotoxin-TP2A | protein | 30 | 0% helix, 33% strand | P83476 |
Ligands and binding sites
- 6OU · [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate · ligand · 16 copies · chains A, D, B, C, H, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.86 | 0.87 | 86 | empty |
| 2 | 257 | 0.59 | 0.79 | 28 | 6OU |
| 3 | 232 | 0.58 | 0.79 | 28 | 6OU |
| 4 | 222 | 0.58 | 0.79 | 29 | 6OU |
| 5 | 263 | 0.54 | 0.76 | 28 | 6OU |
Interfaces
8 interfaces between chains.
- A–D · 1649 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1602 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1591 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1558 Ų buried · 10 hydrogen bonds · protein-protein
- C–G · 510 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 6N4I · Structural basis of Nav1.7 inhibition by a gating-modifier spider toxin · the same entry in another collection · chain F against F, TM-score 1.00
- P83476 · AlphaFold monomer V2.0 prediction for BETA/OMEGA-theraphotoxin-TP2A (P83476) · a predicted model of the same protein · chain E against A, TM-score 0.86
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 P83476
- Elsewhere: RCSB PDB 6N4I · PDBe 6N4I · UniProt P83476
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