SMTL ID : 6sqo.1

Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

hetero-2-2-2-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.9, C.12, R.15, C.32, C.35 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.9, A:C.12, A:C.32, A:C.35 ZN.2: 5 residues within 4Å: Chain A: H.23, H.28, C.46, V.48, C.49 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.23, A:H.28, A:C.46, A:C.49 ZN.6: 4 residues within 4Å: Chain D: C.9, C.12, C.32, C.35 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.9, D:C.12, D:C.32, D:C.35 ZN.7: 5 residues within 4Å: Chain D: H.23, H.28, C.46, V.48, C.49 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.23, D:H.28, D:C.46, D:C.49

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: K.37, M.55, I.56 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain B: A.1, L.2, K.3 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain D: K.37, K.40, M.55, I.56 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain E: A.1, L.2, K.3 Ligand excluded by PLIP

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.5: 3 residues within 4Å: Chain B: R.135, I.136, E.139 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.135, B:R.135, B:E.139 NO3.10: 3 residues within 4Å: Chain E: K.84, R.89, L.118 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.89, E:R.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Magnussen, H.M. et al., Structural basis for DNA damage-induced phosphoregulation of MDM2 RING domain. Nat Commun (2020)

Release Date

2020-05-06

Peptides

E3 ubiquitin-protein ligase Mdm2: AD
Ubiquitin-conjugating enzyme E2 D2: BE
Ubiquitin-40S ribosomal protein S27a: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

E3 ubiquitin-protein ligase Mdm2

Ubiquitin-conjugating enzyme E2 D2

Ubiquitin-40S ribosomal protein S27a

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