NMR-driven structure of the KRAS4B-G12D "alpha-alpha" dimer on a lipid bilayer nanodisc

Structure

solution nmr · 2 distinct chains · 67% helix, 12% strand (DSSP).

Ligands and binding sites

• 7Q9 · [(2~{R})-3-[oxidanyl-[2-(trimethyl-$L^{4}-azanyl) ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] (~{Z})-octadec-9-enoate · ligand · 128 copies · chains A, B, D, E
• 17F · O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine · ligand · 32 copies · chains A, B, D, E
• GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

2 interfaces between chains.

• D–E · 3900 Ų buried · 21 hydrogen bonds · protein-protein
• A–B · 755 Ų buried · 12 hydrogen bonds · protein-protein

Compared structures

• 7RSC · NMR-driven structure of the KRAS4B-G12D alpha-alpha" dimer on a lipid bilayer nanodisc" · the same entry in another collection · chain A against A, TM-score 1.00
• P02647 · AlphaFold monomer V2.0 prediction for apolipoprotein a-I (P02647) · a predicted model of the same protein · chain D against A, TM-score 0.58

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 P01116
• Every structure of UniProt P02647
• Elsewhere: RCSB PDB 7RSC · PDBe 7RSC · UniProt P01116 · UniProt P02647