Crystal structure of the NA+,K+-ATPase in the E2P state with bound MG2+ and anthroylouabain (P2(1)2(1)2(1) symmetry)

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 16% strand (DSSP).

Ligands and binding sites

• PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 11 copies · chains A, B, C, D, E, G
• CLR · Cholesterol · ligand · 5 copies · chains A, B, C, D, E, G
• H0C · [(2~{R},3~{R},4~{R},5~{S},6~{S})-2-[[(1~{R},3~{S}, 5~{S},8~{R},9~{S},10~{R},11~{R},13~{R},14~{S},17~{R})-10-(hydroxymethyl)-13-methyl-1,5,11,14-tetrakis(oxidanyl)-17-(5-oxidanylidene-2~{H}-furan-3-yl)-2,3,4,6,7,8,9,11,12,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthren-3-yl]oxy]-6-methyl-3,5-bis(oxidanyl)oxan-4-yl] anthracene-9-carboxylate · ligand · 2 copies · chains A, C
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains B, D
• MG · Magnesium ion · metal · 4 copies · chains A, C
• NA · Sodium ion · metal · 2 copies · chains A, C

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

Pockets

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

Interfaces

10 interfaces between chains.

• C–D · 2163 Ų buried · 30 hydrogen bonds · protein-protein
• A–B · 2142 Ų buried · 24 hydrogen bonds · protein-protein
• A–G · 796 Ų buried · 4 hydrogen bonds · protein-protein
• C–E · 787 Ų buried · 4 hydrogen bonds · protein-protein
• D–E · 295 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 6 glycan, 2 modified (disulfide, N-glycosylation, phosphorylation).

Compared structures

• 7D93 · Crystal Structure of the Na+,K+-ATPase in the E2P state with bound Mg2+ and… · the same entry in another collection · chain G against G, TM-score 1.00
• P05024 · AlphaFold monomer V2.0 prediction for SODIUM/POTASSIUM-transporting ATPase subunit… · a predicted model of the same protein · chain A against A, TM-score 0.98
• P05027 · AlphaFold monomer V2.0 prediction for SODIUM/POTASSIUM-transporting ATPase subunit beta-1… · a predicted model of the same protein · chain D against A, TM-score 0.97

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 P05024
• Every structure of UniProt P05027
• Every structure of UniProt Q58K79
• Elsewhere: RCSB PDB 7D93 · PDBe 7D93 · UniProt P05024 · UniProt P05027 · UniProt Q58K79