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Crystal structure of human MDM2 in complex with D-peptide inhibitor (DPMI-alpha)

X-ray diffraction
2.4Å resolution
PDB entry 3lnj coloured by chain, front view.
PDB entry 3lnj coloured by chain, side view.
PDB entry 3lnj coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero tetramer (preferred)
Entry contents: 2 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: E3 ubiquitin-protein ligase Mdm2 and peptide
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Multimeric state: hetero tetramer
Accessible surface area: 9801.25 Å2
Buried surface area: 4282.82 Å2
Dissociation area: 906.89 Å2
Dissociation energy (ΔGdiss): 1.5 kcal/mol
Dissociation entropy (TΔSdiss): 11.01 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-163742
Assembly 2
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Assembly Name: E3 ubiquitin-protein ligase Mdm2 and peptide
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Multimeric state: hetero tetramer
Accessible surface area: 9603.98 Å2
Buried surface area: 4590.12 Å2
Dissociation area: 1,371.44 Å2
Dissociation energy (ΔGdiss): 12.66 kcal/mol
Dissociation entropy (TΔSdiss): 14.64 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-163742

Macromolecules

E3 ubiquitin-protein ligase Mdm2
Chains: A, C, E
Length: 85 amino acids
Theoretical weight: 10.04 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q00987 (Residues: 25-109; Coverage: 17%)
Gene name: MDM2
Pfam: SWIB/MDM2 domain
InterPro:
CATH: SWIB/MDM2 domain
E3 ubiquitin-protein ligase Mdm2 in PDB entry 3lnj, assembly 1, front view.
E3 ubiquitin-protein ligase Mdm2 in PDB entry 3lnj, assembly 1, side view.
E3 ubiquitin-protein ligase Mdm2 in PDB entry 3lnj, assembly 1, top view.
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D-peptide inhibitor
Chains: B, D, F
Length: 12 amino acids
Theoretical weight: 1.52 KDa
Source organism: Homo sapiens
Expression system: Not provided
D-peptide inhibitor in PDB entry 3lnj, assembly 1, front view.
D-peptide inhibitor in PDB entry 3lnj, assembly 1, side view.
D-peptide inhibitor in PDB entry 3lnj, assembly 1, top view.
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