11GH | pdb_000011gh

Structure of GMPPNP-bound KRAS-G12C/Y96D, a Switch-II Pocket Inhibitor Resistance Mutant, in Complex with the RAF1 RBD-CRD

• PDB DOI: https://doi.org/10.2210/pdb11GH/pdb

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


• Deposited: 2026-02-22 Released: 2026-10-07 
• Deposition Author(s): Whitley, M.J., Simanshu, D.K.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Models: experimental

Literature

Structural mechanisms underlying resistance to Switch-II pocket inhibitors in KRAS

Whitley, M.J., Dyba, M., Chakrabarti, M., Smith, B.P., Chan, A.H., Denson, J.P., Messing, S.A., Lin, K., Cornilescu, G., Balius, T.E., Nissley, D.V., McCormick, F., Maciag, A.E., Simanshu, D.K.

(2026) Nat Commun 

• DOI: https://doi.org/10.1038/s41467-026-78133-4

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.93 kDa 
• Atom Count: 2,511 
• Modeled Residue Count: 301 
• Deposited Residue Count: 308 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	A	170	Homo sapiens	Mutation(s): 3  Gene Names: KRAS, KRAS2, RASK2 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens) Go to UniProtKB:  P01116
PHAROS:  P01116 GTEx:  ENSG00000133703

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RAF proto-oncogene serine/threonine-protein kinase	B	138	Homo sapiens	Mutation(s): 0  Gene Names: RAF1, RAF EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04049 (Homo sapiens) Explore P04049  Go to UniProtKB:  P04049
PHAROS:  P04049 GTEx:  ENSG00000132155

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP (Subject of Investigation/LOI)	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
ZN	E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAF	B	L-PEPTIDE LINKING	C5 H12 As N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.419	α = 90
b = 133.419	β = 90
c = 89.928	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
EPMR	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-07 
Deposition Author(s): Whitley, M.J., Simanshu, D.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	75N91019D00024

Revision History  

• Version 1.0: 2026-10-07
  Type: Initial release