SMTL ID : 6fge.1

Crystal structure of human ZUFSP/ZUP1 in complex with ubiquitin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.1: 6 residues within 4Å: Chain A: Q.259, H.315, K.316 Chain B: R.42, Q.49 Ligands: EDO.3 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Q.49, B:Q.49, A:Q.259, A:K.316 Salt bridges: B:R.42, A:H.315 Water bridges: A:H.315, A:H.315

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

EDO.2: 4 residues within 4Å: Chain A: Y.200, H.211, I.212, T.343 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.212, A:I.212 Water bridges: A:T.343, A:T.343 EDO.3: 4 residues within 4Å: Chain A: K.314, H.315, K.316 Ligands: MLI.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.316 EDO.4: 10 residues within 4Å: Chain A: F.215, H.216, K.217, T.219, H.225, P.226, R.227, L.228, I.347, P.348 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.217, A:H.225, A:R.227, A:L.228, A:I.347

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: Y.45, M.74, S.77, L.78, F.82, D.83, D.84, C.159 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.45, A:M.74, A:D.83, A:D.84 Water bridges: A:Y.45, A:R.133 GOL.6: 2 residues within 4Å: Chain A: S.218, G.223 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.218 Water bridges: A:S.218, A:G.223, A:H.315

7 x FMT: FORMIC ACID(Non-functional Binders)

FMT.7: 3 residues within 4Å: Chain A: Y.37, W.193, G.260 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.37 FMT.8: 4 residues within 4Å: Chain A: G.220, P.221, P.226, M.310 No protein-ligand interaction detected (PLIP) FMT.9: 5 residues within 4Å: Chain A: S.121, K.126, G.127, W.128 Ligands: NH4.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.121, A:G.127, A:W.128 FMT.10: 5 residues within 4Å: Chain A: H.216, K.316, Q.317 Chain B: D.39, R.42 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.317 FMT.11: 3 residues within 4Å: Chain A: D.169, K.172, E.173 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.169 FMT.12: 5 residues within 4Å: Chain A: G.81, F.82, M.155, L.156, P.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.156 FMT.17: 2 residues within 4Å: Chain A: F.342 Chain B: R.72 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:Q.319, A:A.344, B:L.73

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 4 residues within 4Å: Chain A: K.304, R.307, S.309, N.312 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.304, A:N.312

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.14: 5 residues within 4Å: Chain A: S.121, C.130, P.283 Chain B: X.76 Ligands: FMT.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.121, A:P.283 NH4.15: 3 residues within 4Å: Chain A: S.121, S.122, L.123 No protein-ligand interaction detected (PLIP)

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

ACT.16: 6 residues within 4Å: Chain A: Y.37, L.39, L.183 Chain B: V.70, L.71, R.74 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.71 Salt bridges: B:R.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwasna, D. et al., Discovery and Characterization of ZUFSP/ZUP1, a Distinct Deubiquitinase Class Important for Genome Stability. Mol. Cell (2018)

Release Date

2018-04-04

Peptides

Zinc finger with UFM1-specific peptidase domain protein: A
Polyubiquitin-B: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Zinc finger with UFM1-specific peptidase domain protein

Polyubiquitin-B

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