SMTL ID : 5mnj.1 (1 other biounit)

Structure of MDM2-MDMX-UbcH5B-ubiquitin complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain C: C.33, C.36, C.56, C.59 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.33, C:C.36, C:C.56, C:C.59 ZN.2: 4 residues within 4Å: Chain C: H.47, H.52, C.70, C.73 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.47, C:H.52, C:C.70, C:C.73 ZN.3: 5 residues within 4Å: Chain D: C.11, C.14, R.17, C.34, C.37 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.11, D:C.14, D:C.34, D:C.37 ZN.4: 4 residues within 4Å: Chain D: H.25, H.30, C.48, C.51 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.25, D:H.30, D:C.48, D:C.51

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain D: A.46, S.47, K.52 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.47 Water bridges: D:K.52, D:K.52 Salt bridges: D:K.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nomura, K. et al., Structural analysis of MDM2 RING separates degradation from regulation of p53 transcription activity. Nat. Struct. Mol. Biol. (2017)

Release Date

2017-05-31

Peptides

Ubiquitin-conjugating enzyme E2 D2: A
Polyubiquitin-B: B
E3 ubiquitin-protein ligase Mdm2: C
Protein Mdm4: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Ubiquitin-conjugating enzyme E2 D2

Polyubiquitin-B

E3 ubiquitin-protein ligase Mdm2

Protein Mdm4

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