MolNFT v1 · #189989 · protein
Cryo-EM structure of human NAV1.7-BETA1-BETA2 complex at 2.2 ångström resolution
7W9K · Sodium channel protein type 9 subunit alpha: “Cryo-EM structure of human NAV1.7-BETA1-BETA2 complex at 2.2 ångström resolution”. Electron microscopy, 8 ligands (LPE, Y01, PCW), 20 pockets (best druggability 0.83). MolNFT v1 #189989…
- PDB
- 7W9K
- Type
- protein
- Length
- 1,705 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, 9Z9, 1PW, NAG, NA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 59% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium channel protein type 9 subunit alpha | protein | 1413 | 68% 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
- LPE · 1-O-octadecyl-sn-glycero-3-phosphocholine · ligand · 15 copies · chains A, B
- Y01 · Cholesterol hemisuccinate · ligand · 6 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 · 3 copies · chains A
- 9Z9 · (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en · ligand · chains A
- 1PW · (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- NA · Sodium ion · metal · chains 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.83 | 0.86 | 72 | 9Z9 |
| 2 | 528 | 0.69 | 0.79 | 63 | empty |
| 3 | 179 | 0.68 | 0.86 | 22 | 1PW |
| 4 | 163 | 0.67 | 0.87 | 18 | LPE |
| 5 | 364 | 0.67 | 0.81 | 51 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2054 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 263 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 7W9K · Cryo-EM structure of human Nav1.7-beta1-beta2 complex at 2.2 angstrom resolution · 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 0.92
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 7W9K · PDBe 7W9K · UniProt Q15858 · UniProt Q07699 · UniProt O60939
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