Research workbench
Structure of NavMS pore and C-terminal domain crystallised in the presence of channel blocking compound
Analyse Structure of NavMS pore and C-terminal domain crystallised in the presence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PA6
- Type
- protein
- Length
- 364 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.36
- Source
- Magnetococcus sp.
- Molecule
- Ion transport protein
- UniProt
- A0L5S6
- Ligands
- 2CV, NA
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · resolution 3.36 · 3 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ion transport protein | protein | 92 | 77% helix, 0% strand | A0L5S6 |
| B | Ion transport protein | protein | 90 | 79% helix, 0% strand | A0L5S6 |
| C, D | Ion transport protein | protein | 91 | 80% helix, 0% strand | A0L5S6 |
Ligands and binding sites
- 2CV · Hega-10 · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains C, D
- 12P · Dodecaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.73 | 0.75 | 95 | 2CV |
Interfaces
5 interfaces between chains.
- C–D · 713 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 685 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 201 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 201 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 55 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4PA6 · Structure of navms pore and C-terminal domain crystallised in the presence of channel… · 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 4PA6 · PDBe 4PA6 · UniProt A0L5S6
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