› 5tb5

X-ray diffraction
2Å resolution

Crystal structure of full-length farnesylated and methylated KRAS4b in complex with PDE-delta (crystal form I - with partially disordered hypervariable region)

Released:
DOI: 10.2210/pdb5tb5/pdb
PDB 5tb5 coloured by chain and viewed from the front.
PDB 5tb5 coloured by chain and viewed from the side.
PDB 5tb5 coloured by chain and viewed from the top.
Source organism: Homo sapiens
Primary publication:
Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ.
Dharmaiah S, Bindu L, Tran TH, Gillette WK, Frank PH, Ghirlando R, Nissley DV, Esposito D, McCormick F, Stephen AG, Simanshu DK
Proc Natl Acad Sci U S A 113 E6766-E6775 (2016)
PMID: 27791178

Function and Biology Details

Reaction catalysed: 
GTP + H(2)O = GDP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
GTPase KRas Chains: A, C
Molecule details ›
Chains: A, C
Length: 185 amino acids
Theoretical weight: 21.06 KDa
Source organism: Homo sapiens
Expression system: unidentified baculovirus
UniProt:
  • Canonical: P01116 (Residues: 2-186; Coverage: 97%)
  • Best match: P01116-2 (Residues: 2-185)
Gene names: KRAS, KRAS2, RASK2
Sequence domains: Ras family
Structure domains: P-loop containing nucleotide triphosphate hydrolases
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta Chains: B, D
Molecule details ›
Chains: B, D
Length: 150 amino acids
Theoretical weight: 17.44 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43924 (Residues: 1-150; Coverage: 100%)
Gene names: PDE6D, PDED
Sequence domains: GMP-PDE, delta subunit
Structure domains: GMP phosphodiesterase, delta subunit

Ligands and Environments

3 bound ligands:
Ligand FAR 2 x FAR
Ligand GDP 2 x GDP
Ligand EDO 2 x EDO
1 modified residue:
Ligand CMT 2 x CMT

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 58.386Å b: 70.651Å c: 94.307Å
α: 90° β: 92.4° γ: 90°
R-values:
R R work R free
0.205 0.201 0.248
Expression systems:
  • unidentified baculovirus
  • Escherichia coli

Quick links

Citations

15 review citations

A Non-Canonical Calmodulin Target Motif Comprising a Polybasic Region and Lipidated Terminal Residue Regulates Localization.
Grant et al. (2020)
14 more

2 mentions without citation

Targeting the α4-α5 interface of RAS results in multiple levels of inhibition.
Spencer-Smith et al. (2019)
1 more