MolNFT v1 · #137011 · protein
Crystal structure of the navab voltage-gated sodium channel in a closed conformation
5VB2 · Ion transport protein: “Crystal structure of the navab voltage-gated sodium channel in a closed conformation”. X-ray diffraction, 4 ligands (PX4, CPS, PO4), 20 pockets (best druggability 0.84). MolNFT v1 #137011 on GenesisL1: 3D…
- PDB
- 5VB2
- Type
- protein
- Length
- 1,050 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ion transport protein
- UniProt
- A8EVM5
- Ligands
- PX4, CPS, PO4, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 87% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ion transport protein | protein | 262 | 87% helix, 0% strand | A8EVM5 |
| B | Ion transport protein | protein | 259 | 87% helix, 0% strand | A8EVM5 |
| C | Ion transport protein | protein | 261 | 88% helix, 0% strand | A8EVM5 |
| D | Ion transport protein | protein | 268 | 85% helix, 0% strand | A8EVM5 |
Ligands and binding sites
- PX4 · 1,2-dimyristoyl-sn-glycero-3-phosphocholine · ligand · 13 copies · chains A, D, B, C
- CPS · 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate · ligand · 8 copies · chains A, D, B, C
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A, B, C, D
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 | 523 | 0.84 | 0.89 | 54 | empty |
| 2 | 134 | 0.70 | 0.90 | 21 | empty |
| 3 | 101 | 0.66 | 0.89 | 19 | empty |
| 4 | 110 | 0.66 | 0.88 | 18 | empty |
| 5 | 391 | 0.60 | 0.75 | 33 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2522 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2453 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 2407 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 2273 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 191 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5VB2 · Crystal structure of the NavAb voltage-gated sodium channel in a closed conformation · 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
- Elsewhere: RCSB PDB 5VB2 · PDBe 5VB2 · UniProt A8EVM5
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