› 4zfi

X-ray diffraction
2Å resolution

Structure of Mdm2 with low molecular weight inhibitor

Released:
DOI: 10.2210/pdb4zfi/pdb
PDB entry 4zfi coloured by chain, front view.
PDB entry 4zfi coloured by chain, side view.
PDB entry 4zfi coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A Unique Mdm2-Binding Mode of the 3-Pyrrolin-2-one- and 2-Furanone-Based Antagonists of the p53-Mdm2 Interaction.
Surmiak E, Twarda-Clapa A, Zak KM, Musielak B, Tomala MD, Kubica K, Grudnik P, Madej M, Jablonski M, Potempa J, Kalinowska-Tluscik J, Dömling A, Dubin G, Holak TA
ACS Chem Biol 11 3310-3318 (2016)
PMID: 27709883

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-169499 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
E3 ubiquitin-protein ligase Mdm2 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 97 amino acids
Theoretical weight: 11.4 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q00987 (Residues: 18-113; Coverage: 20%)
Gene name: MDM2
Sequence domains: SWIB/MDM2 domain
Structure domains: SWIB/MDM2 domain

Ligands and Environments

1 bound ligand:
Ligand 4NJ 4 x 4NJ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 66.36Å b: 70.25Å c: 96.44Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.243
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Proteasomal Degradation of Zn-Dependent Hdacs: The E3-Ligases Implicated and the Designed Protacs That Enable Degradation.
Márquez-Cantudo et al. (2021)
12 other articles

3 mentions without citation

A Hybrid Docking and Machine Learning Approach to Enhance the Performance of Virtual Screening Carried out on Protein-Protein Interfaces.
Singh et al. (2022)
2 more