9EW4 | pdb_00009ew4

Ternary structure of 14-3-3s, C-RAF phosphopeptide 12mer (pS259) and compound 86 (1124384)

• PDB DOI: https://doi.org/10.2210/pdb9EW4/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-03 Released: 2025-04-16 
• Deposition Author(s): Konstantinidou, M., Vickery, H., Pennings, M.A.M., Virta, J., Visser, E.J., Oetelaar, M.C.M., Overmans, M., Neitz, J., Ottmann, C., Brunsveld, L., Arkin, M.R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.211 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Small molecule stabilization of the 14-3-3sigma/CRAF complex inhibits the MAPK pathway

Konstantinidou, M., Vickery, H., Pennings, M.A.M., Virta, J., Visser, E.J., Oetelaar, M.C.M., Overmans, M., Neitz, J., Ottmann, C., Brunsveld, L., Arkin, M.R.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content 

• Total Structure Weight: 28.19 kDa 
• Atom Count: 2,188 
• Modeled Residue Count: 245 
• Deposited Residue Count: 245 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein sigma	A	236	Homo sapiens	Mutation(s): 0  Gene Names: SFN, HME1
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens) Explore P31947  Go to UniProtKB:  P31947
PHAROS:  P31947 GTEx:  ENSG00000175793

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RAF proto-oncogene serine/threonine-protein kinase	B [auth P]	9	Homo sapiens	Mutation(s): 0  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
WQ9 (Subject of Investigation/LOI)	G [auth A]	1-[(5~{R})-2-(4-bromanyl-3-fluoranyl-phenyl)sulfonyl-2,7-diazaspiro[4.4]nonan-7-yl]-2-chloranyl-ethanone C15 H17 Br Cl F N2 O3 S RVTGGWFEHOZRDJ-OAHLLOKOSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A], E [auth A], F [auth A], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	B [auth P]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.211 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.874	α = 90
b = 112.61	β = 90
c = 62.992	γ = 90

Software Package:

Software Name	Purpose
PDB-REDO	refinement
autoPROC	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Konstantinidou, M., Vickery, H., Pennings, M.A.M., Virta, J., Visser, E.J., Oetelaar, M.C.M., Overmans, M., Neitz, J., Ottmann, C., Brunsveld, L., Arkin, M.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM147696

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release