SMTL ID : 7oje.1 (1 other biounit)

Crystal structure of the covalent complex between Tribolium castaneum deubiquitinase ZUP and Ubiquitin-PA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-1-1-mer

Ligands

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 6 residues within 4Å: Chain A: R.331, R.334, K.335, S.336, A.339 Ligands: NA.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.334, A:R.334, A:S.336 Water bridges: A:R.334, A:K.335 Salt bridges: A:R.331, A:K.335

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

EDO.2: 6 residues within 4Å: Chain A: H.285, R.290, A.339, M.340, A.342, Y.345 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.290, A:R.290, A:Y.345 Water bridges: A:K.341 EDO.3: 3 residues within 4Å: Chain A: S.146, Y.147, R.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.146, A:R.150 EDO.7: 5 residues within 4Å: Chain A: Y.62, Q.215 Chain B: V.70, L.71, R.74 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.71, B:R.74 Water bridges: B:L.8, A:Q.215

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.10, C.13, H.29, H.33 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.10, A:C.13, A:H.29, A:H.33

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 3 residues within 4Å: Chain A: R.331, R.334 Ligands: CIT.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.335, A:K.335 NA.6: 5 residues within 4Å: Chain A: N.66, Q.67, G.68, R.219, N.222 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.68, A:R.219 Water bridges: A:G.68, A:N.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hermanns, T. et al., A structural basis for the diverse linkage specificities within the ZUFSP deubiquitinase family. Nat Commun (2022)

Release Date

2022-02-02

Peptides

Lys-63-specific deubiquitinase ZUFSP: A
Polyubiquitin-B: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lys-63-specific deubiquitinase ZUFSP

Polyubiquitin-B

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