7AD0 | pdb_00007ad0

X-ray structure of Mdm2 with modified p53 peptide

• PDB DOI: https://doi.org/10.2210/pdb7AD0/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-09-13 Released: 2020-10-28 
• Deposition Author(s): Twarda-Clapa, A., Fortuna, P., Grudnik, P., Dubin, G., Berlicki, L., Holak, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.238 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Systematic ""foldamerization"" of peptide inhibiting p53-MDM2/X interactions by the incorporation of trans- or cis-2-aminocyclopentanecarboxylic acid residues

Fortuna, P., Twarda-Clapa, A., Skalniak, L., Ozga, K., Holak, T.A., Berlicki, L.

(2020) Eur J Med Chem 208: 112814

• DOI: https://doi.org/10.1016/j.ejmech.2020.112814

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 73.16 kDa 
• Atom Count: 5,145 
• Modelled Residue Count: 608 
• Deposited Residue Count: 624 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A, B, C, D, E, F	90	Homo sapiens	Mutation(s): 0  Gene Names: MDM2 EC: 2.3.2.27
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
Modified p53 peptide	G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M]	14	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.238 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.811	α = 90
b = 76.082	β = 90
c = 197.299	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-10-28 
Deposition Author(s): Twarda-Clapa, A., Fortuna, P., Grudnik, P., Dubin, G., Berlicki, L., Holak, T.A.

Revision History  

• Version 1.0: 2020-10-28
  Type: Initial release
  
• Version 1.1: 2022-10-26
  Changes: Database references
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-01-31
  Changes: Refinement description