SMTL ID : 9egv.1 (2 other biounits)

HOIL-1 RING2 domain bound to ubiquitin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-1-mer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.38, Q.40, C.41, C.56, V.58, C.59 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.38, A:C.41, A:C.56, A:C.59 ZN.2: 9 residues within 4Å: Chain A: C.64, V.66, T.67, R.71, C.84, C.86, C.93, C.100 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.64, A:C.84, A:C.93, A:C.100 ZN.3: 6 residues within 4Å: Chain A: C.86, R.87, C.93, C.97, C.100 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.86, A:C.93, A:C.97, A:C.100 ZN.5: 8 residues within 4Å: Chain B: C.38, Q.40, C.41, I.43, C.56, V.58, C.59, T.61 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.38, B:C.41, B:C.56, B:C.59 ZN.6: 9 residues within 4Å: Chain B: C.64, V.66, T.67, R.71, C.84, C.86, C.93, C.100 Ligands: ZN.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:C.84, B:C.93, B:C.100 ZN.7: 6 residues within 4Å: Chain B: V.66, C.86, C.93, C.97, C.100 Ligands: ZN.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.86, B:C.93, B:C.97, B:C.100

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

CL.4: 5 residues within 4Å: Chain A: T.61, E.62, W.72, G.76, P.77 Ligand excluded by PLIP

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

SO4.8: 2 residues within 4Å: Chain B: W.53, R.55 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.55 SO4.9: 3 residues within 4Å: Chain B: R.87, Q.98, N.99 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.98 Salt bridges: B:R.87 SO4.10: 6 residues within 4Å: Chain A: R.37 Chain C: K.18, L.20, T.21, G.22, H.80 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Water bridges: A:R.37, A:R.37 Salt bridges: A:R.37, C:K.18, C:H.80 Hydrogen bonds: C:L.20, C:G.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, X.S. et al., The RBR E3 ubiquitin ligase HOIL-1 can ubiquitinate diverse non-protein substrates in vitro. Biorxiv (2024)

Release Date

2024-12-11

Peptides

RanBP-type and C3HC4-type zinc finger-containing protein 1: AB
Polyubiquitin-C: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

RanBP-type and C3HC4-type zinc finger-containing protein 1

Polyubiquitin-C

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