Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 54.97 kDa 
• Atom Count: 4196 
• Residue Count: 478 
• Unique protein chains: 2

5J31

Crystal structure of 14-3-3zeta in complex with an alkyne cross-linked cyclic peptide derived from ExoS

• DOI: 10.2210/pdb5J31/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-03-30 Released: 2016-10-19 
• Deposition Author(s): Wallraven, K., Cromm, P., Bier, D., Glas, A., Grossmann, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.219 
• R-Value Work: 0.163 
• R-Value Observed: 0.166 

Literature

Constraining an Irregular Peptide Secondary Structure through Ring-Closing Alkyne Metathesis.

Cromm, P.M., Wallraven, K., Glas, A., Bier, D., Furstner, A., Ottmann, C., Grossmann, T.N.

(2016) Chembiochem 17: 1915-1919

• PubMed: 27596722 
• DOI: 10.1002/cbic.201600362
• Primary Citation of Related Structures:  
  5J31


• PubMed Abstract: 
  

Macrocyclization can be used to constrain peptides in their bioactive conformations, thereby supporting target affinity and bioactivity. In particular, for the targeting of challenging protein-protein interactions, macrocyclic peptides have proven to be very useful. Available approaches focus on the stabilization of α-helices, which limits their general applicability. Here we report for the first time on the use of ring-closing alkyne metathesis for the stabilization of an irregular peptide secondary structure. A small library of alkyne-crosslinked peptides provided a number of derivatives with improved target affinity relative to the linear parent peptide. In addition, we report the crystal structure of the highest-affinity derivative in a complex with its protein target 14-3-3ζ. It can be expected that the alkyne-based macrocyclization of irregular binding epitopes should give rise to new scaffolds suitable for targeting of currently intractable proteins.

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Organizational Affiliation: 

Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein zeta/delta	A, B	230	Homo sapiens	Mutation(s): 0  Gene Names: YWHAZ
Find proteins for P63104 (Homo sapiens) Explore P63104  Go to UniProtKB:  P63104
NIH Common Fund Data Resources
PHAROS  P63104 GTEx  ENSG00000164924

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Exoenzyme S	C, D	10	Pseudomonas aeruginosa	Mutation(s): 1  Gene Names: exoS
Find proteins for Q93SQ3 (Pseudomonas aeruginosa) Explore Q93SQ3  Go to UniProtKB:  Q93SQ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEZ	B	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MK8	C,D	L-PEPTIDE LINKING	C7 H15 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.219 
• R-Value Work: 0.163 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.94	α = 90
b = 105.58	β = 90
c = 114.51	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-03-30 
• Released Date: 2016-10-19 
Deposition Author(s): Wallraven, K., Cromm, P., Bier, D., Glas, A., Grossmann, T.

Revision History 

• Version 1.0: 2016-10-19
  Type: Initial release
  
• Version 1.1: 2016-10-26
  Changes: Database references