PDBe 5mnj

X-ray diffraction
2.16Å resolution

Structure of MDM2-MDMX-UbcH5B-ubiquitin complex

Released:

Function and Biology Details

Reactions catalysed:
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
(1a) S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [(E3-independent) E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-monoubiquitinyl-[(E3-independent) ubiquitin-conjugating enzyme]-L-cysteine
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:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Ubiquitin-conjugating enzyme E2 D2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 147 amino acids
Theoretical weight: 16.85 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62837 (Residues: 1-147; Coverage: 100%)
  • Best match: P62837-2 (Residues: 1-118)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
Ubiquitin Chains: B, F
Molecule details ›
Chains: B, F
Length: 81 amino acids
Theoretical weight: 8.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family
E3 ubiquitin-protein ligase Mdm2 Chains: C, G
Molecule details ›
Chains: C, G
Length: 86 amino acids
Theoretical weight: 9.67 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q00987 (Residues: 428-491; Coverage: 13%)
Gene name: MDM2
Sequence domains: Zinc finger, C3HC4 type (RING finger)
Protein Mdm4 Chains: D, H
Molecule details ›
Chains: D, H
Length: 64 amino acids
Theoretical weight: 7.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O15151 (Residues: 427-490; Coverage: 13%)
Gene names: MDM4, MDMX
Sequence domains: Zinc finger, C3HC4 type (RING finger)

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P1
Unit cell:
a: 54.24Å b: 62.76Å c: 66.35Å
α: 69.83° β: 69.22° γ: 78.21°
R-values:
R R work R free
0.192 0.19 0.231
Expression system: Escherichia coli