NMR data-driven model of GTPase KRAS-GMPPNP:CMPD2 complex tethered to a nanodisc

Structure

solution nmr · 2 distinct chains · 66% helix, 10% strand (DSSP).

Ligands and binding sites

• PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 64 copies · chains A, B, C
• 17F · O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine · ligand · 16 copies · chains B, A, C
• GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains B
• EWS · (2R,4S)-4-[(5-bromo-1H-indole-3-carbonyl)amino]-2-[(4-chlorophenyl)methyl]piperidin-1-ium · ligand · chains B
• MG · Magnesium ion · metal · chains B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–C · 3430 Ų buried · 67 hydrogen bonds · protein-protein

Compared structures

• 6CC9 · NMR data-driven model of GTPase KRas-GMPPNP:Cmpd2 complex tethered to a 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 C against A, TM-score 0.57

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 6CC9 · PDBe 6CC9 · UniProt P02647 · UniProt P01116