› 5xco

X-ray diffraction
1.25Å resolution

Crystal structure of human K-Ras G12D Mutant in complex with GDP and Cyclic Inhibitory Peptide

Released:
DOI: 10.2210/pdb5xco/pdb
PDB entry 5xco coloured by chain, front view.
PDB entry 5xco coloured by chain, side view.
PDB entry 5xco coloured by chain, top view.
Source organisms:
Primary publication:
Crystal Structure of a Human K-Ras G12D Mutant in Complex with GDP and the Cyclic Inhibitory Peptide KRpep-2d.
Sogabe S, Kamada Y, Miwa M, Niida A, Sameshima T, Kamaura M, Yonemori K, Sasaki S, Sakamoto JI, Sakamoto K
ACS Med Chem Lett 8 732-736 (2017)
PMID: 28740607

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)
Assembly name:
PDBe Complex ID:
PDB-CPX-134012 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
GTPase KRas, N-terminally processed Chain: A
Molecule details ›
Chain: A
Length: 171 amino acids
Theoretical weight: 19.47 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01116 (Residues: 1-169; Coverage: 89%)
Gene names: KRAS, KRAS2, RASK2
Sequence domains: Ras family
Structure domains: P-loop containing nucleotide triphosphate hydrolases
ACE-ARG-ARG-ARG-ARG-CYS-PRO-LEU-TYR-ILE-SER-TYR-ASP-PRO-VAL-CYS-ARG-ARG-ARG-ARG-NH2 Chain: B
Molecule details ›
Chain: B
Length: 21 amino acids
Theoretical weight: 2.55 KDa
Source organism: Escherichia phage T7
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand GDP 1 x GDP
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P3121
Unit cell:
a: 51.529Å b: 51.529Å c: 129.741Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.172 0.171 0.194
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

The current understanding of KRAS protein structure and dynamics.
Pantsar T. (2020)
5 more

9 mentions without citation

Structure-based inhibitor design of mutant RAS proteins-a paradigm shift.
Nyíri et al. (2020)
8 more