SMTL ID : 4ao5.1 (1 other biounit)

B. subtilis prophage dUTPase YosS in complex with dUMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

3 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.1: 10 residues within 4Å: Chain A: Q.75, N.77, G.80, V.81, I.82, Y.86, W.93, F.94, P.96 Chain C: S.65 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:I.82, A:Y.86 Hydrogen bonds: A:Q.75, A:N.77, A:F.94, A:F.94, C:S.65 Water bridges: A:V.81, A:V.81, C:S.65, C:S.66, C:S.66 pi-Stacking: A:F.94 UMP.3: 10 residues within 4Å: Chain A: S.65 Chain B: Q.75, N.77, G.80, V.81, I.82, Y.86, W.93, F.94, P.96 16 PLIP interactions: 10 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.82, B:Y.86 Hydrogen bonds: B:Q.75, B:N.77, B:F.94, B:F.94, A:S.65 Water bridges: B:V.81, B:V.81, B:Y.86, A:S.65, A:S.65, A:S.65, A:S.66, A:S.66 pi-Stacking: B:F.94 UMP.5: 9 residues within 4Å: Chain B: S.65, S.66 Chain C: N.77, G.80, I.82, Y.86, W.93, F.94, P.96 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain C Hydrogen bonds: B:S.65, B:S.65, C:Q.75, C:N.77, C:F.94, C:F.94 Water bridges: B:S.65, B:S.65, B:S.66, C:V.81, C:Y.86 Hydrophobic interactions: C:Y.86

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

NA.2: 5 residues within 4Å: Chain A: I.18, N.19, I.27, D.28, R.30 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.19, A:N.19, A:D.28, A:R.30 Water bridges: A:R.110 NA.4: 2 residues within 4Å: Chain B: T.16, G.108 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.14, B:T.16 Water bridges: B:T.16 NA.6: 2 residues within 4Å: Chain C: R.30, R.110 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.30, C:R.110, C:R.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcia-Nafria, J. et al., Tying Down the Arm in Bacillus Dutpase: Structure and Mechanism. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-04-03

Peptides

SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEO TIDOHYDROLASE YOSS: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEO TIDOHYDROLASE YOSS

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