5AFG | pdb_00005afg

Structure of the Stapled Peptide Bound to Mdm2

• PDB DOI: https://doi.org/10.2210/pdb5AFG/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-01-22 Released: 2016-01-27 
• Deposition Author(s): Lau, Y.H., Wu, Y., Rossmann, M., de Andrade, P., Tan, Y.S., McKenzie, G.J., Venkitaraman, A.R., Hyvonen, M., Spring, D.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.226 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Double Strain-Promoted Macrocyclization for the Rapid Selection of Cell-Active Stapled Peptides.

Lau, Y.H., Wu, Y., Rossmann, M., Tan, B.X., De Andrade, P., Tan, Y.S., Verma, C., Mckenzie, G.J., Venkitaraman, A.R., Hyvonen, M., Spring, D.R.

(2015) Angew Chem Int Ed Engl 54: 15410

• PubMed: 26768531 
• DOI: https://doi.org/10.1002/anie.201508416
• Primary Citation Related Structures: 
  5AFG


• PubMed Abstract: 
  

  Peptide stapling is a method for designing macrocyclic alpha-helical inhibitors of protein-protein interactions. However, obtaining a cell-active inhibitor can require significant optimization. We report a novel stapling technique based on a double strain-promoted azide-alkyne reaction, and exploit its biocompatibility to accelerate the discovery of cell-active stapled peptides. As a proof of concept, MDM2-binding peptides were stapled in parallel, directly in cell culture medium in 96-well plates, and simultaneously evaluated in a p53 reporter assay. This in situ stapling/screening process gave an optimal candidate that showed improved proteolytic stability and nanomolar binding to MDM2 in subsequent biophysical assays. α-Helicity was confirmed by a crystal structure of the MDM2-peptide complex. This work introduces in situ stapling as a versatile biocompatible technique with many other potential high-throughput biological applications.

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Organizational Affiliation: 
• Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW (UK).
Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA (UK).
p53Lab, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648 (Singapore).
Bioinformatics Institute, A*STAR, 30 Biopolis St, #07-01 Matrix, Singapore 138671 (Singapore).
Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.
School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551.
Hutchison/MRC Research Centre, Hills Rd, Cambridge CB2 0XZ (UK).
Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW (UK). [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 12.87 kDa 
• Atom Count: 913 
• Modeled Residue Count: 95 
• Deposited Residue Count: 109 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 UBIQUITIN-PROTEIN LIGASE MDM2	A	97	Homo sapiens	Mutation(s): 2  EC: 6.3.2.19 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens) Explore Q00987  Go to UniProtKB:  Q00987
PHAROS:  Q00987 GTEx:  ENSG00000135679

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
STAPLED PEPTIDE	B	12	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P07	C [auth B]	1,8-DIETHYL-1,8-DIHYDRODIBENZO[3,4:7,8][1,2,3]TRIAZOLO[4',5':5,6]CYCLOOCTA[1,2-D][1,2,3]TRIAZOLE C20 H18 N6 YRZRZRBFIALCLI-MKVCYXFSSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LAY	B	L-PEPTIDE LINKING	C8 H15 N O3		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.226 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.821	α = 90
b = 36.821	β = 90
c = 177.416	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PROTEUM2	data reduction
PROTEUM2	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-27 
Deposition Author(s): Lau, Y.H., Wu, Y., Rossmann, M., de Andrade, P., Tan, Y.S., McKenzie, G.J., Venkitaraman, A.R., Hyvonen, M., Spring, D.R.

Revision History  

• Version 1.0: 2016-01-27
  Type: Initial release
  
• Version 2.0: 2019-05-15
  Changes: Data collection, Derived calculations, Other, Polymer sequence
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description