SMTL ID : 2xy3.2 (1 other biounit)

Structure of the Bacillus subtilis prophage dUTPase with dUpNHpp

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-trimer

Ligands

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

DUP.1: 8 residues within 4Å: Chain A: N.74, G.77, V.78, I.79, Y.83, F.91, P.93 Chain C: S.62 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.62, A:N.74 Water bridges: C:S.62, C:S.62 Hydrophobic interactions: A:Y.83 DUP.2: 14 residues within 4Å: Chain A: R.61, S.62, S.63, Q.110 Chain B: Q.72, N.74, G.77, V.78, I.79, Y.83, W.90, F.91, P.93 Ligands: MG.3 17 PLIP interactions: 9 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:I.79, B:Y.83 Hydrogen bonds: B:Q.72, B:N.74, B:F.91, B:F.91, A:R.61, A:S.62, A:S.62, A:S.62, A:S.63, A:S.63, A:Q.110 Water bridges: B:V.78, B:V.78, A:Q.110 pi-Stacking: B:F.91 DUP.4: 14 residues within 4Å: Chain B: R.61, S.62, S.63, Q.110 Chain C: Q.72, N.74, G.77, V.78, I.79, Y.83, W.90, F.91, P.93 Ligands: MG.5 20 PLIP interactions: 9 interactions with chain B, 11 interactions with chain C Hydrogen bonds: B:R.61, B:S.62, B:S.62, B:S.62, B:S.63, B:S.63, B:Q.110, C:Q.72, C:N.74, C:V.78, C:D.80, C:F.91, C:F.91 Water bridges: B:Q.110, C:V.78, C:V.78 Salt bridges: B:R.61 Hydrophobic interactions: C:I.79, C:Y.83 pi-Stacking: C:F.91

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.3: 1 residues within 4Å: Ligands: DUP.2 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: D.25 Ligands: DUP.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcia-Nafria, J. et al., The Structure of Bacillus Subtilis Sp Beta Prophage Dutpase and its Complexes with Two Nucleotides. Acta Crystallogr.,Sect.D (2011)

Release Date

2011-02-23

Peptides

SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS

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