Macromolecule Content

Total Structure Weight: 20.02 kDa
Atom Count: 1611
Modelled Residue Count: 170
Deposited Residue Count: 170
Unique protein chains: 1

7OK3

Crystal Structure of KRasG13C in Complex with Nucleotide-based Covalent Inhibitor edaGDP

PDB DOI: 10.2210/pdb7OK3/pdb

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

Deposited: 2021-05-17 Released: 2022-08-03
Deposition Author(s): Goebel, L., Mueller, M.P., Rauh, D.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.200
R-Value Work: 0.158
R-Value Observed: 0.160

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Targeting oncogenic KRasG13C with nucleotide-based covalent inhibitors

Goebel, L., Kirschner, T., Koska, S., Rai, A., Janning, P., Maffini, S., Vatheuer, H., Czodrowski, P., Goody, R.S., Mueller, M.P., Rauh, D.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2B of GTPase KRas	A	170	Homo sapiens	Mutation(s): 4 Gene Names: KRAS, KRAS2, RASK2 EC: 3.6.5.2
UniProt
Find proteins for P01116-2 (Homo sapiens) Explore P01116-2 Go to UniProtKB: P01116-2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01116-2
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VJ8 (Subject of Investigation/LOI) Query on VJ8 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	edaGDP C₁₆ H₂₅ N₇ O₁₃ P₂ ZYFFWDLDVKYDIX-FRJWGUMJSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.200
R-Value Work: 0.158
R-Value Observed: 0.160
Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.4	α = 90
b = 73.4	β = 90
c = 54.2	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Deposited Date: 2021-05-17
Released Date: 2022-08-03

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	RA 1055/5-1
German Research Foundation (DFG)	Germany	GO 284/10-1

Revision History (Full details and data files)

Version 1.0: 2022-08-03
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.