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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.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.226 (Depositor), 0.230 (DCC)
- R-Value Work: 0.176 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.179 (Depositor)
Starting Model:experimental
View more details
Download MendeleyDouble 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 Search on PubMedSearch on PubMed Central
- DOI: https://doi.org/10.1002/anie.201508416
- Primary Citation of 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.
- 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). spring@ch.cam.ac.uk.
Organizational Affiliation:
Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (P07)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Hetero 2-mer - A1B1
Find Similar Assemblies
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
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| E3 UBIQUITIN-PROTEIN LIGASE MDM2 | 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 Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q00987 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| STAPLED PEPTIDE | 12 | synthetic construct | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| P07 Query on P07 Download Ideal Coordinates CCD File | 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 Query on LAY | B | L-PEPTIDE LINKING | C8 H15 N O3 |  | LEU |
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.226 (Depositor), 0.230 (DCC)
- R-Value Work: 0.176 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.179 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 36.821 | α = 90 |
| b = 36.821 | β = 90 |
| c = 177.416 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PROTEUM2 | data reduction |
| PROTEUM2 | data scaling |
| PHASER | phasing |
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 (Full details and data files)
- 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
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