SMTL ID : 5nz2.1

Twist and induce: Dissecting the link between the enzymatic activity and the SaPI inducing capacity of the phage 80 dUTPase. D95E mutant from dUTPase 80alpha phage.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-trimer

Ligands

3 x DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE(Non-covalent)

DUP.1: 14 residues within 4Å: Chain A: G.78, K.79, I.80, D.81, Y.84, N.87, L.88, G.89, N.91 Chain B: R.64, S.65, G.66, Q.137 Ligands: MG.2 14 PLIP interactions: 7 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:N.20, B:R.64, B:S.65, B:S.65, B:G.66, B:Q.137, A:D.81, A:Y.84, A:G.89, A:G.89 Salt bridges: B:R.64 Hydrophobic interactions: A:I.80, A:Y.84 Water bridges: A:N.91 DUP.3: 14 residues within 4Å: Chain B: G.78, K.79, I.80, D.81, Y.84, N.87, L.88, G.89, N.91 Chain C: R.64, S.65, G.66, Q.137 Ligands: MG.4 15 PLIP interactions: 7 interactions with chain C, 8 interactions with chain B Hydrogen bonds: C:N.20, C:R.64, C:S.65, C:S.65, C:G.66, C:Q.137, B:D.81, B:D.81, B:Y.84, B:G.89, B:G.89 Salt bridges: C:R.64 Hydrophobic interactions: B:I.80, B:Y.84 Water bridges: B:N.91 DUP.5: 14 residues within 4Å: Chain A: R.64, S.65, G.66, Q.137 Chain C: G.78, K.79, I.80, D.81, Y.84, N.87, L.88, G.89, N.91 Ligands: MG.6 13 PLIP interactions: 6 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:I.80, C:Y.84 Hydrogen bonds: C:D.81, C:G.89, C:G.89, A:N.20, A:R.64, A:S.65, A:S.65, A:G.66, A:Q.137 Water bridges: C:N.91 Salt bridges: A:R.64

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain B: D.28, R.64, Q.137 Ligands: DUP.1 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain C: D.28, R.64, Q.137 Ligands: DUP.3 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain A: D.28, R.64, Q.137 Ligands: DUP.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alite, C. et al., Dissecting the link between the enzymatic activity and the SaPI inducing capacity of the phage 80 alpha dUTPase. Sci Rep (2017)

Release Date

2017-09-20

Peptides

DUTPase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

DUTPase

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