MolNFT v1 · #189991 · protein
Cryo-EM structure of human NAV1.7(E406K) in complex with auxiliary beta subunits, protx-II and tetrodotoxin (S6IV pi helix conformer)
7W9M · Sodium channel protein type 9 subunit alpha: “Cryo-EM structure of human NAV1.7(E406K) in complex with auxiliary beta subunits, protx-II and tetrodotoxin…”. Electron microscopy, 5 ligands (Y01, 9SR, P5S), 20 pockets (best…
- PDB
- 7W9M
- Type
- protein
- Length
- 1,710 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium channel protein type 9 subunit alpha; Sodium channel subunit beta-1; Sodium…
- UniProt
- Q15858, Q07699, O60939
- Ligands
- Y01, 9SR, P5S, LPE, NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 58% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium channel protein type 9 subunit alpha | protein | 1418 | 67% helix, 4% strand | Q15858 |
| B | Sodium channel subunit beta-1 | protein | 173 | 25% helix, 36% strand | Q07699 |
| C | Sodium channel subunit beta-2 | protein | 119 | 8% helix, 46% strand | O60939 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 5 copies · chains A
- 9SR · (1R,5R,6R,7R,9S,11S,12S,13S,14S)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diazatetracyclo[7.3.1.1~7,11~.0~1,6~]tetradec-3-ene-5, 9,12,13,14-pentol (non-preferred name) · ligand · chains A
- P5S · O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy) propyl]oxy}(hydroxy)phosphoryl]-L-serine · ligand · chains A
- LPE · 1-O-octadecyl-sn-glycero-3-phosphocholine · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 992 | 0.86 | 0.87 | 90 | empty |
| 2 | 643 | 0.72 | 0.79 | 73 | empty |
| 3 | 505 | 0.70 | 0.79 | 37 | empty |
| 4 | 100 | 0.64 | 0.88 | 17 | empty |
| 5 | 350 | 0.62 | 0.78 | 44 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2114 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 269 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 7W9M · Cryo-EM structure of human Nav1.7(E406K) in complex with auxiliary beta subunits… · the same entry in another collection · chain A against A, TM-score 1.00
- O60939 · AlphaFold monomer V2.0 prediction for sodium channel subunit beta-2 (O60939) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q07699 · AlphaFold monomer V2.0 prediction for sodium channel subunit beta-1 (Q07699) · a predicted model of the same protein · chain B against A, TM-score 0.92
- Q15858 · AlphaFold monomer V2.0 prediction for sodium channel protein type 9 subunit alpha (Q15858) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 Q15858
- Every structure of UniProt Q07699
- Every structure of UniProt O60939
- Elsewhere: RCSB PDB 7W9M · PDBe 7W9M · UniProt Q15858 · UniProt Q07699 · UniProt O60939
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