Crystal structure of full-length farnesylated and methylated KRAS4B in complex with pde-delta (crystal form I - with partially disordered hypervariable region)

Structure

x-ray diffraction · 4 distinct chains · 28% helix, 40% strand (DSSP).

Ligands and binding sites

• FAR · Farnesyl · ligand · 2 copies · chains A, B, C, D
• GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, C
• EDO · 1,2-ethanediol · additive · 2 copies · chains B, D

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

Pockets

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

Interfaces

2 interfaces between chains.

• C–D · 749 Ų buried · 11 hydrogen bonds · protein-protein
• A–B · 688 Ų buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 lipid, 2 modified (farnesylation, nonstandard).

Compared structures

• 5TB5 · Crystal structure of full-length farnesylated and methylated KRAS4b in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
• O43924 · AlphaFold monomer V2.0 prediction for retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic… · 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 P01116
• Every structure of UniProt O43924
• Elsewhere: RCSB PDB 5TB5 · PDBe 5TB5 · UniProt P01116 · UniProt O43924