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

Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 catalytic domain bound to ubiquitin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.118, C.159, H.166, H.168 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.118, A:C.159, A:H.166, A:H.168 ZN.2: 5 residues within 4Å: Chain A: H.103, H.105, S.113, D.116 Chain B: G.81 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.103, A:H.105, A:D.116, A:D.116, B:G.81

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

PO4.3: 3 residues within 4Å: Chain A: K.171, T.174, M.175 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.174, A:T.174, A:M.175 Salt bridges: A:K.171

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

EDO.4: 5 residues within 4Å: Chain A: I.144, V.176, Q.178, V.182, E.184 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.184, A:E.184 Water bridges: A:K.32, A:I.144, A:V.176, A:Q.178 EDO.5: 5 residues within 4Å: Chain A: E.73, T.78, C.79, G.80 Chain B: R.79 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.79, A:T.78, A:C.79 Water bridges: B:G.80, A:E.73 EDO.6: 8 residues within 4Å: Chain A: I.52, L.87, Q.91, T.98, Y.123 Chain B: L.13, L.76 Ligands: EDO.8 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:L.76, B:L.76, A:T.98, A:T.98 EDO.7: 5 residues within 4Å: Chain A: D.77, Q.108, F.111, F.165 Chain B: G.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.77, A:Q.108 EDO.8: 7 residues within 4Å: Chain A: Y.123 Chain B: T.12, L.13, L.74, V.75, L.76 Ligands: EDO.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.13, B:L.74, B:L.76 EDO.9: 6 residues within 4Å: Chain A: F.88, D.92 Chain B: K.11, T.12, L.13, H.73 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.92, A:D.92, B:K.11 Water bridges: A:N.95

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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