7XKJ | pdb_00007xkj

Kras-G12D-GDP-MRTX1133 by FIB-MicroED

• PDB DOI: https://doi.org/10.2210/pdb7XKJ/pdb

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


• Deposited: 2022-04-19 Released: 2023-08-02 
• Deposition Author(s): Li, X.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 3.00 Å
• R-Value Free: 
  0.337 (Depositor), 0.349 (DCC) 
• R-Value Work: 
  0.310 (Depositor), 0.324 (DCC) 
• R-Value Observed: 
  0.313 (Depositor) 

Starting Model: experimental

Literature

Kras-G12D-GDP-MRTX1133 by FIB-MicroED

Li, X.M.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 20.38 kDa 
• Atom Count: 1,409 
• Modeled Residue Count: 168 
• Deposited Residue Count: 169 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KRAS proto-oncogene, GTPase	A	169	Homo sapiens	Mutation(s): 2  Gene Names: mMyoMyo1_007468 EC: 3.6.5.2
UniProt
Find proteins for A0A7J7Z4L6 (Myotis myotis) Explore A0A7J7Z4L6  Go to UniProtKB:  A0A7J7Z4L6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6IC (Subject of Investigation/LOI)	C [auth A]	4-(4-[(1R,5S)-3,8-diazabicyclo[3.2.1]octan-3-yl]-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-7-yl)-5-ethynyl-6-fluoronaphthalen-2-ol C33 H31 F3 N6 O2 SCLLZBIBSFTLIN-INOGPEIASA-N
GDP (Subject of Investigation/LOI)	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 3.00 Å
• R-Value Free:  0.337 (Depositor), 0.349 (DCC) 
• R-Value Work:  0.310 (Depositor), 0.324 (DCC) 
• R-Value Observed: 0.313 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.88	α = 90
b = 49.28	β = 90
c = 87.2	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-02 
Deposition Author(s): Li, X.M.

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Funding Organization	Location	Grant Number
Not funded	China	--

Revision History  

• Version 1.0: 2023-08-02
  Type: Initial release
  
• Version 1.1: 2023-08-16
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2025-09-17
  Changes: Advisory, Derived calculations, Refinement description, Structure summary