5UK9

Wild-type K-Ras(GCP) pH 6.5

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

K-Ras Populates Conformational States Differently from Its Isoform H-Ras and Oncogenic Mutant K-RasG12D.

Parker, J.A., Volmar, A.Y., Pavlopoulos, S., Mattos, C.

(2018) Structure 26: 810

  • DOI: 10.1016/j.str.2018.03.018
  • Primary Citation of Related Structures:  
    5UK9

  • PubMed Abstract: 

    • Structures of wild-type K-Ras from crystals obtained in the presence of guanosine triphosphate (GTP) or its analogs have remained elusive. Of the K-Ras mutants, only K-RasG12D and K-RasQ61H are available in the PDB representing the activated form of the ...

    Structures of wild-type K-Ras from crystals obtained in the presence of guanosine triphosphate (GTP) or its analogs have remained elusive. Of the K-Ras mutants, only K-RasG12D and K-RasQ61H are available in the PDB representing the activated form of the GTPase not in complex with other proteins. We present the crystal structure of wild-type K-Ras bound to the GTP analog GppCH 2 p, with K-Ras in the state 1 conformation. Signatures of conformational states obtained by one-dimensional proton NMR confirm that K-Ras has a more substantial population of state 1 in solution than H-Ras, which predominantly favors state 2. The oncogenic mutant K-RasG12D favors state 2, changing the balance of conformational states in favor of interactions with effector proteins. Differences in the population of conformational states between K-Ras and H-Ras, as well as between K-Ras and its mutants, can provide a structural basis for focused targeting of the K-Ras isoform in cancer-specific strategies.

    Organizational Affiliation: 

    Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115, USA. Electronic address: c.mattos@northeastern.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase KRas A, B166Homo sapiensMutation(s): 0 
Gene Names: KRAS, KRAS2, RASK2
EC: 3.6.5.2
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
NIH Common Fund Data Resources
PHAROS:  P01116
GTEx:  ENSG00000133703
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP
Download Ideal Coordinates CCD File 
B
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N		 Ligand Interaction
GDP
Query on GDP
Download Ideal Coordinates CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.107α = 90
b = 87.553β = 90
c = 93.692γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data collection
HKL-3000data scaling
PHENIXmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-1517295

Revision History 

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2018-05-30
    Changes: Data collection, Database references
  • Version 1.2: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence