MolNFT v1 · #189994 · protein
Cryo-EM structure of human NAV1.7(E406K) in complex with auxiliary beta subunits, huwentoxin-IV and saxitoxin (S6IV alpha helix conformer)
7W9T · Sodium channel protein type 9 subunit alpha: “Cryo-EM structure of human NAV1.7(E406K) in complex with auxiliary beta subunits, huwentoxin-IV and saxitoxin…”. Electron microscopy, 7 ligands (LPE, Y01, PCW), 20 pockets (best…
- PDB
- 7W9T
- Type
- protein
- Length
- 1,709 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
- LPE, Y01, PCW, P5S, 9SL, 9Z9, NAG
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 3 distinct chains · 60% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium channel protein type 9 subunit alpha | protein | 1417 | 68% helix, 4% strand | Q15858 |
| B | Sodium channel subunit beta-1 | protein | 173 | 25% helix, 32% strand | Q07699 |
| C | Sodium channel subunit beta-2 | protein | 119 | 8% helix, 47% strand | O60939 |
Ligands and binding sites
- LPE · 1-O-octadecyl-sn-glycero-3-phosphocholine · ligand · 14 copies · chains A, B
- Y01 · Cholesterol hemisuccinate · ligand · 5 copies · chains A
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 5 copies · chains A
- P5S · O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy) propyl]oxy}(hydroxy)phosphoryl]-L-serine · ligand · 2 copies · chains A
- 9SL · [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate · ligand · chains A
- 9Z9 · (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 546 | 0.80 | 0.86 | 62 | 9Z9 |
| 2 | 469 | 0.68 | 0.79 | 58 | empty |
| 3 | 450 | 0.67 | 0.79 | 52 | empty |
| 4 | 132 | 0.67 | 0.88 | 16 | empty |
| 5 | 460 | 0.66 | 0.78 | 34 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2022 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 272 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 8 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 7W9T · 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
- 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 0.93
- 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
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 7W9T · PDBe 7W9T · UniProt Q15858 · UniProt Q07699 · UniProt O60939
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