SMTL ID : 4msm.2 (1 other biounit)

Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 E286A mutant bound to ubiquitin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

hetero-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.103, H.105, D.116 Chain B: G.81 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.103, A:H.105, A:D.116, A:D.116, H2O.7 ZN.2: 5 residues within 4Å: Chain A: H.118, C.159, H.166, H.168 Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.118, A:C.159, A:H.166, A:H.168

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

EDO.3: 3 residues within 4Å: Chain A: L.36, P.137, N.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.140 EDO.4: 5 residues within 4Å: Chain A: K.56, R.58, F.63, T.65 Ligands: PO4.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.58 Water bridges: A:K.188 EDO.5: 6 residues within 4Å: Chain A: K.20, Q.124, L.125, P.128, D.149, L.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.20, A:K.20, A:Q.124 EDO.6: 6 residues within 4Å: Chain A: H.118, C.159, R.160, K.161, H.166 Ligands: ZN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.160 Water bridges: A:H.118 EDO.7: 5 residues within 4Å: Chain A: E.73, G.80, T.81, T.82 Chain B: R.79 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.73 EDO.9: 6 residues within 4Å: Chain A: T.98 Chain B: T.12, L.13, L.74, V.75, L.76 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:L.13, B:L.76, A:T.98, A:T.98

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 1 residues within 4Å: Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.188, A:K.188 Salt bridges: A:K.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shrestha, R.K. et al., Insights into the Mechanism of Deubiquitination by JAMM Deubiquitinases from Cocrystal Structures of the Enzyme with the Substrate and Product. Biochemistry (2014)

Release Date

2014-06-18

Peptides

AMSH-like protease sst2: A
Ubiquitin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

AMSH-like protease sst2

Ubiquitin

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