6YE9 | pdb_00006ye9

Small-molecule inhibitor of 14-3-3 protein-protein interactions

• PDB DOI: https://doi.org/10.2210/pdb6YE9/pdb

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


• Deposited: 2020-03-24 Released: 2021-03-31 
• Deposition Author(s): Ottmann, C., Visser, E.J.
• Funding Organization(s): Netherlands Organisation for Scientific Research (NWO), German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Structure-based conversion of a promiscuous inhibitor to a selective stabilizer of protein-protein interactions

Sijbesma, E., Visser, E.J., Plitzko, K., Thiel, P., Milroy, L.G., Kaiser, M., Brunsveld, L., Ottmann, C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26.94 kDa 
• Atom Count: 2,206 
• Modelled Residue Count: 236 
• Deposited Residue Count: 236 
• Unique protein chains: 1

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OO8 (Subject of Investigation/LOI)	E [auth A]	[2-[2-oxidanylidene-2-[(phenylmethyl)amino]ethoxy]phenyl]phosphonic acid C15 H16 N O5 P LOUYKKOJKVDPIE-UHFFFAOYSA-N
MG	B [auth A], C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.836	α = 90
b = 112.795	β = 90
c = 62.715	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-31 
Deposition Author(s): Ottmann, C., Visser, E.J.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	024.001.035
Netherlands Organisation for Scientific Research (NWO)	Netherlands	016.150.336
Netherlands Organisation for Scientific Research (NWO)	Netherlands	711.018.003
German Research Foundation (DFG)	Netherlands	CRC1093

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 1.1: 2021-04-14
  Changes: Derived calculations
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description