Crystal structure of the light-driven sodium pump KR2 in the pentameric "wet" form

Structure

x-ray diffraction · 1 distinct chain · 76% helix, 3% strand (DSSP).

Ligands and binding sites

• LFA · Eicosane · ligand · 35 copies · chains A, B, E, C, D
• RET · Retinal · ligand · 5 copies · chains A, B, C, D, E
• NA · Sodium ion · metal · 5 copies · chains A, B, E, C, D
• OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 23 copies · chains A, B, E, C, D
• BOG · octyl beta-D-glucopyranoside · additive · 5 copies · chains A, B, C, D, E

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

Pockets

16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• B–C · 1323 Ų buried · 8 hydrogen bonds · protein-protein
• C–D · 1322 Ų buried · 8 hydrogen bonds · protein-protein
• A–B · 1315 Ų buried · 8 hydrogen bonds · protein-protein
• A–E · 1303 Ų buried · 9 hydrogen bonds · protein-protein
• D–E · 1300 Ų buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 cofactor (retinal Schiff base).

Compared structures

• 6RF1 · Crystal structure of the light-driven sodium pump KR2 in the pentameric "wet" form · 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 N0DKS8
• Elsewhere: RCSB PDB 6RF1 · PDBe 6RF1 · UniProt N0DKS8