8CPR

G13D mutant of KRAS4b (2-169) bound to GDP with the switch-I in fully open conformation crystallized in sodium potassium phosphate buffer

• PDB DOI: https://doi.org/10.2210/pdb8CPR/pdb

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-03-03 Released: 2024-06-12 
• Deposition Author(s): Moche, M., Jungholm, O., Strandback, E., Ampah-Korsah, H., Nyman, T., Orwar, O.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.248 
• R-Value Work: 0.179 
• R-Value Observed: 0.183 

Starting Model: experimental

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 8BLR

Literature

A G13D open-state-selective anti-KRAS antibody shows in vivo anti-cancer activity

Moche, M., Jungholm, O., Strandback, E., Nyman, T., Orwar, O., Ampah-Korsah, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.93 kDa 
• Atom Count: 1,650 
• Modelled Residue Count: 168 
• Deposited Residue Count: 170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas, N-terminally processed	A	170	Homo sapiens	Mutation(s): 1  Gene Names: KRAS, KRAS2, RASK2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens) Explore P01116  Go to UniProtKB:  P01116
PHAROS:  P01116 GTEx:  ENSG00000133703

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.248 
• R-Value Work: 0.179 
• R-Value Observed: 0.183 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.413	α = 90
b = 76.413	β = 90
c = 55.862	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
STARANISO	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): Moche, M., Jungholm, O., Strandback, E., Ampah-Korsah, H., Nyman, T., Orwar, O.

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Funding Organization	Location	Grant Number
Other government	Sweden	C33001013

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release