SMTL ID : 4nql.1

The crystal structure of the DUB domain of AMSH orthologue, Sst2 from S. pombe, in complex with lysine 63-linked diubiquitin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.142, C.183, H.190, H.192 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.142, A:C.183, A:H.190, A:H.192

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

EDO.2: 9 residues within 4Å: Chain A: I.76, L.111, Q.115, T.122, Y.147 Chain B: L.8, V.70, L.71 Ligands: EDO.7 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.115, A:T.122, A:T.122, B:L.71, B:L.71 EDO.3: 5 residues within 4Å: Chain A: N.70, S.100, D.101, T.131, Q.132 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.70, A:S.100, A:T.131, A:T.131, A:Q.132 EDO.4: 6 residues within 4Å: Chain A: E.97, T.99, T.102, C.103, G.104 Chain B: R.74 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.102, A:C.103 Water bridges: A:A.98, A:T.99, A:T.99 EDO.5: 5 residues within 4Å: Chain A: G.167, I.168, M.199, V.200, Q.202 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.168, A:V.200, A:Q.202 EDO.6: 6 residues within 4Å: Chain A: K.44, Q.148, L.149, P.152, D.173, L.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.44 EDO.7: 8 residues within 4Å: Chain A: Y.147, M.150 Chain B: T.7, L.8, L.69, V.70, L.71 Ligands: EDO.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.8, B:L.71 EDO.8: 5 residues within 4Å: Chain A: F.135 Chain C: Q.62, K.63, E.64, S.65 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.65

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

2014-10-08

Peptides

AMSH-like protease sst2: A
Ubiquitin: B
Ubiquitin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

AMSH-like protease sst2

Ubiquitin

Ubiquitin

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