SMTL ID : 5xiu.1

Crystal structure of RNF168 UDM2 in complex with Lys63-linked diubiquitin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 3 residues within 4Å: Chain A: L.23, H.27, E.30 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:E.64, A:R.26, A:E.30, A:E.30 EDO.2: 3 residues within 4Å: Chain A: F.24, H.27, K.28 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.24, A:K.28 EDO.3: 9 residues within 4Å: Chain A: L.40, Q.41, E.43, D.45 Chain B: R.42, V.70, L.71, R.72, L.73 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Water bridges: A:Q.41, A:D.45, A:D.45, A:K.46, B:L.73 Hydrogen bonds: B:R.42, B:R.42, B:L.73 EDO.4: 6 residues within 4Å: Chain A: Q.41 Chain B: T.7, L.8, T.9, L.69, L.71 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.7, B:L.8, B:T.9, B:T.9, B:L.69 EDO.5: 4 residues within 4Å: Chain B: K.48, R.54, D.58, Y.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.54 Water bridges: B:D.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takahashi, T.S. et al., Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168. Nat Commun (2018)

Release Date

2018-03-07

Peptides

E3 ubiquitin-protein ligase RNF168: A
Ubiquitin-40S ribosomal protein S27a: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E3 ubiquitin-protein ligase RNF168

Ubiquitin-40S ribosomal protein S27a

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