5VPI

Crystal structure of human KRAS G12A mutant in complex with GTP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Structural insight into the rearrangement of the switch I region in GTP-bound G12A K-Ras.

Xu, S., Long, B.N., Boris, G.H., Chen, A., Ni, S., Kennedy, M.A.

(2017) Acta Crystallogr D Struct Biol 73: 970-984

  • DOI: 10.1107/S2059798317015418
  • Primary Citation of Related Structures:  
    5VP7, 5VPI, 5VPY, 5VPZ, 5VQ0, 5VQ1, 5VQ2, 5VQ6, 5VQ8, 5W22

  • PubMed Abstract: 

    • K-Ras, a molecular switch that regulates cell growth, apoptosis and metabolism, is activated when it undergoes a conformation change upon binding GTP and is deactivated following the hydrolysis of GTP to GDP. Hydrolysis of GTP in water is accelerated by coordination to K-Ras, where GTP adopts a high-energy conformation approaching the transition state ...

    K-Ras, a molecular switch that regulates cell growth, apoptosis and metabolism, is activated when it undergoes a conformation change upon binding GTP and is deactivated following the hydrolysis of GTP to GDP. Hydrolysis of GTP in water is accelerated by coordination to K-Ras, where GTP adopts a high-energy conformation approaching the transition state. The G12A mutation reduces intrinsic K-Ras GTP hydrolysis by an unexplained mechanism. Here, crystal structures of G12A K-Ras in complex with GDP, GTP, GTPγS and GppNHp, and of Q61A K-Ras in complex with GDP, are reported. In the G12A K-Ras-GTP complex, the switch I region undergoes a significant reorganization such that the Tyr32 side chain points towards the GTP-binding pocket and forms a hydrogen bond to the GTP γ-phosphate, effectively stabilizing GTP in its precatalytic state, increasing the activation energy required to reach the transition state and contributing to the reduced intrinsic GTPase activity of G12A K-Ras mutants.

    Organizational Affiliation: 

    Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase KRasA, B170Homo sapiensMutation(s): 2 
Gene Names: KRAS, KRAS2, RASK2
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.792α = 90
b = 94.792β = 90
c = 121.48γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-20
    Changes: Database references