Structure of the na+ unbound rotor ring modified with N,N F- dicyclohexylcarbodiimide of the na+-transporting V-ATPase

Structure

x-ray diffraction · 1 distinct chain · 85% helix, 1% strand (DSSP).

Ligands and binding sites

• DCW · Dicyclohexylurea · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
• UMQ · Undecyl-maltoside · ligand · 2 copies · chains C, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

10 interfaces between chains.

• H–I · 1739 Ų buried · 3 hydrogen bonds · protein-protein
• A–B · 1739 Ų buried · 4 hydrogen bonds · protein-protein
• F–G · 1739 Ų buried · 2 hydrogen bonds · protein-protein
• C–D · 1734 Ų buried · 4 hydrogen bonds · protein-protein
• A–J · 1731 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 covalent (covalent ligand).

Compared structures

• 3AOU · Structure of the Na+ unbound rotor ring modified with N,N f-Dicyclohexylcarbodiimide of… · the same entry in another collection · chain J against J, TM-score 1.00
• P43457 · AlphaFold monomer V2.0 prediction for V-type sodium ATPase subunit K (P43457) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P43457
• Elsewhere: RCSB PDB 3AOU · PDBe 3AOU · UniProt P43457