9U5T | pdb_00009u5t

GDP-bound KRAS G12D in complex with MCB-294

• PDB DOI: https://doi.org/10.2210/pdb9U5T/pdb

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-03-21 Released: 2025-07-30 
• Deposition Author(s): Li, K.K., Guo, R.-T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.211 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

GDP-bound KRAS G12D in complex with MCB-294

Li, K.K., Guo, R.-T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 20.92 kDa 
• Atom Count: 1,641 
• Modeled Residue Count: 170 
• Deposited Residue Count: 175 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2B of GTPase KRas	A	175	Homo sapiens	Mutation(s): 1  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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	D [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.211 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.037	α = 90
b = 95.037	β = 90
c = 121.012	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SAINT	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Li, K.K., Guo, R.-T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release