NMR-driven structure of KRAS4B-GDP homodimer on a lipid bilayer nanodisc

Structure

solution nmr · 2 distinct chains · 69% helix, 11% strand (DSSP).

Ligands and binding sites

• PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 64 copies · chains A, B, C, D
• 17F · O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine · ligand · 16 copies · chains B, D, C
• GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, C
• MG · Magnesium ion · metal · 2 copies · chains B, C

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

2 interfaces between chains.

• A–D · 3726 Ų buried · 54 hydrogen bonds · protein-protein
• B–C · 1103 Ų buried · 11 hydrogen bonds · protein-protein

Compared structures

• 6W4F · NMR-driven structure of KRAS4B-GDP homodimer 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 A 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 P02647
• Every structure of UniProt P01116
• Elsewhere: RCSB PDB 6W4F · PDBe 6W4F · UniProt P02647 · UniProt P01116