SMTL ID : 5y5p.1 (1 other biounit)

Crystal structure of the dUTPase of white spot syndrome virus in complex with dU,PPi and Mg2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-trimer

Ligands

3 x DUR: 2'-DEOXYURIDINE(Non-covalent)

DUR.1: 14 residues within 4Å: Chain A: T.87, G.88, T.89, I.90, D.91, Y.94, E.97, L.98, K.99, R.164, G.168, F.169 Chain B: S.75 Ligands: POP.2 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.90, A:Y.94 Hydrogen bonds: A:T.89, A:D.91, A:D.91, A:K.99, A:K.99, A:F.169, B:S.75 Water bridges: A:D.91 DUR.5: 14 residues within 4Å: Chain B: T.87, G.88, T.89, I.90, D.91, Y.94, E.97, L.98, K.99, R.164, G.168, F.169 Chain C: S.75 Ligands: POP.6 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.90, B:Y.94 Hydrogen bonds: B:T.89, B:D.91, B:D.91, B:K.99, B:K.99, B:F.169, C:S.75, C:S.75 Water bridges: B:I.101 DUR.8: 12 residues within 4Å: Chain A: S.75 Chain C: T.87, G.88, T.89, I.90, D.91, Y.94, E.97, L.98, K.99, I.101 Ligands: POP.3 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.90, C:Y.94 Hydrogen bonds: C:T.89, C:D.91, C:Y.94, C:K.99, C:K.99, A:S.75

3 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.2: 11 residues within 4Å: Chain A: R.164, G.168, F.169, G.170, S.171, T.172 Chain B: R.74, S.75, G.76 Ligands: DUR.1, MG.4 15 PLIP interactions: 7 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:G.170, A:S.171, A:T.172, B:S.75, B:G.76 Water bridges: A:R.164, A:R.164, A:T.172, B:R.74, B:R.74, B:M.77, B:Q.121 Salt bridges: A:R.164, B:R.74, B:R.74 POP.3: 4 residues within 4Å: Chain A: R.74, S.75, G.76 Ligands: DUR.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.75, A:G.76, A:Q.121 Water bridges: A:M.77 Salt bridges: A:R.74, A:R.74 POP.6: 11 residues within 4Å: Chain B: R.164, G.168, F.169, G.170, S.171, T.172 Chain C: R.74, S.75, G.76 Ligands: DUR.5, MG.7 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.170, B:S.171, B:T.172, C:S.75, C:G.76 Water bridges: B:T.172, B:T.172 Salt bridges: B:R.164, C:R.74, C:R.74

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain A: R.164 Ligands: POP.2 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: R.164 Chain C: Q.121 Ligands: POP.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zang, K. et al., The dUTPase of white spot syndrome virus assembles its active sites in a noncanonical manner. J. Biol. Chem. (2018)

Release Date

2017-12-06

Peptides

Wsv112: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Wsv112

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