Research workbench
Structure of navms in complex with channel blocking compound
Analyse Structure of navms in complex with channel blocking compound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PA3
- Type
- protein
- Length
- 366 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ion transport protein
- UniProt
- A0L5S6
- Ligands
- 2CV, NA, BR
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ion transport protein | protein | 92 | 82% helix, 0% strand | A0L5S6 |
| B | Ion transport protein | protein | 90 | 81% helix, 0% strand | A0L5S6 |
| C | Ion transport protein | protein | 93 | 80% helix, 0% strand | A0L5S6 |
| D | Ion transport protein | protein | 91 | 79% helix, 0% strand | A0L5S6 |
Ligands and binding sites
- 2CV · Hega-10 · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 6 copies · chains A, B
- BR · Bromide ion · ion · 2 copies · chains B, D
- 12P · Dodecaethylene glycol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.62 | 0.77 | 37 | 2CV |
| 2 | 152 | 0.52 | 0.78 | 21 | empty |
| 3 | 154 | 0.47 | 0.76 | 22 | 2CV |
| 4 | 103 | 0.40 | 0.76 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 668 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 614 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 138 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 137 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 54 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4PA3 · Structure of NavMS in complex with channel blocking compound · 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 A0L5S6
- Elsewhere: RCSB PDB 4PA3 · PDBe 4PA3 · UniProt A0L5S6
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