SMTL ID : 3pt2.2 (1 other biounit)

Structure of a viral OTU domain protease bound to Ubiquitin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: M.53, N.55, T.57, S.60 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.57, A:T.57 SO4.4: 2 residues within 4Å: Chain B: K.48, R.54 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.48, B:R.54 SO4.5: 7 residues within 4Å: Chain A: L.84, V.85 Chain B: R.72, R.74 Chain C: G.41, N.100, W.102 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Salt bridges: B:R.72, B:R.74 Hydrogen bonds: C:N.100 SO4.6: 4 residues within 4Å: Chain C: M.53, N.55, T.57, S.60 1 PLIP interactions: 1 interactions with chain C Water bridges: C:T.57 SO4.9: 2 residues within 4Å: Chain D: K.48, R.54 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:K.48, D:R.54 SO4.10: 7 residues within 4Å: Chain A: G.41, N.100, W.102 Chain C: L.84, V.85 Chain D: R.72, R.74 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:N.100 Salt bridges: D:R.72, D:R.74

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 1 residues within 4Å: Chain A: T.52 No protein-ligand interaction detected (PLIP) ACT.7: 1 residues within 4Å: Chain C: T.52 No protein-ligand interaction detected (PLIP)

2 x 4LJ: 1.7.6 3-bromanylpropan-1-amine(Covalent)

4LJ.3: 8 residues within 4Å: Chain A: D.40, G.41, C.43, W.102, T.153, H.154 Chain B: G.75 Chain D: D.39 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.153 4LJ.8: 8 residues within 4Å: Chain B: D.39 Chain C: D.40, G.41, C.43, W.102, T.153, H.154 Chain D: G.75 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

James, T.W. et al., Structural basis for the removal of ubiquitin and interferon-stimulated gene 15 by a viral ovarian tumor domain-containing protease. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-01-19

Peptides

RNA polymerase: AC
Ubiquitin B: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

RNA polymerase

Ubiquitin B

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