9S84 | pdb_00009s84

Crystal structure of KRAS G12D D38C (GDP-bound)

• PDB DOI: https://doi.org/10.2210/pdb9S84/pdb

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


• Deposited: 2025-08-05 Released: 2026-06-10 
• Deposition Author(s): Zak, K.M., Kessler, D.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.185 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Starting Model: experimental

Literature

KRAS G12D D38C Structure

Zak, K.M., Kessler, D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 19.94 kDa 
• Atom Count: 1,667 
• Modeled Residue Count: 170 
• Deposited Residue Count: 170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog, isoform CRA_b	A	170	Homo sapiens	Mutation(s): 2  Gene Names: KRAS, hCG_14731 EC: 3.6.5.2
UniProt
Find proteins for A0ABF7PHA5 (Homo sapiens) Explore A0ABF7PHA5  Go to UniProtKB:  A0ABF7PHA5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	E [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.185 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.978	α = 90
b = 66.978	β = 90
c = 89.466	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-10 
Deposition Author(s): Zak, K.M., Kessler, D.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-06-10
  Type: Initial release