Crystal structure of rotor ring with dccd of the V- ATPase from enterococcus hirae

Structure

x-ray diffraction · 1 distinct chain · 86% helix, 0% strand (DSSP).

Ligands and binding sites

• LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 20 copies · chains A, J, B, C, D, E, F, G, H, I
• DCW · Dicyclohexylurea · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
• UMQ · Undecyl-maltoside · ligand · 10 copies · chains A, J, C, D, E, F, G, H, I
• NA · Sodium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J

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.

• D–E · 1748 Ų buried · 3 hydrogen bonds · protein-protein
• G–H · 1747 Ų buried · 4 hydrogen bonds · protein-protein
• A–B · 1739 Ų buried · 3 hydrogen bonds · protein-protein
• B–C · 1739 Ų buried · 3 hydrogen bonds · protein-protein
• E–F · 1738 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 2DB4 · Crystal structure of rotor ring with DCCD of the V- ATPase from Enterococcus hirae · 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 2DB4 · PDBe 2DB4 · UniProt P43457