SMTL ID : 7m4n.1 (1 other biounit)

Crystal structure of RBR E3 ligase RNF216 in complex with K63-linked di-ubiquitin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

hetero-1-2-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.29, C.32, C.47, C.49 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.29, A:C.32, A:C.47, A:C.49 ZN.2: 4 residues within 4Å: Chain A: C.54, C.57, H.66, C.84 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.54, A:C.57, A:H.66, A:C.84 ZN.3: 4 residues within 4Å: Chain A: C.68, H.70, C.78, C.81 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.68, A:H.70, A:C.78, A:C.81

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

SO4.4: 2 residues within 4Å: Chain A: H.70, R.83 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.70, A:R.83 SO4.5: 3 residues within 4Å: Chain A: S.73, P.74 Chain C: K.48 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.48 SO4.7: 5 residues within 4Å: Chain A: R.25, E.95 Chain B: G.47, K.48, Q.49 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.95, B:Q.49, B:Q.49 Salt bridges: A:R.25 SO4.8: 2 residues within 4Å: Chain C: R.42, R.72 4 PLIP interactions: 4 interactions with chain C Water bridges: C:R.72, C:R.72 Salt bridges: C:R.42, C:R.72

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: S.39, E.40, G.41 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.40, A:E.40, A:G.41, A:G.41, A:D.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cotton, T.R. et al., Structural basis of K63-ubiquitin chain formation by the Gordon-Holmes syndrome RBR E3 ubiquitin ligase RNF216. Mol.Cell (2022)

Release Date

2022-01-05

Peptides

E3 ubiquitin-protein ligase RNF216: A
Ubiquitin: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

E3 ubiquitin-protein ligase RNF216

Ubiquitin

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