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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.238 (Depositor), 0.249 (DCC)
R-Value Work:
0.187 (Depositor), 0.195 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7AD0

This is version 2.1 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A, B, C, D, E 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00987
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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] 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), 0.249 (DCC)
R-Value Work: 0.187 (Depositor), 0.195 (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

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Entry History

Deposition Data

Released Date: 2020-10-28

Deposition Author(s):

Twarda-Clapa, A.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.