SMTL ID : 1seh.1 (1 other biounit)

Crystal structure of E. coli dUTPase complexed with the product dUMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-trimer

Ligands

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

UMP.1: 12 residues within 4Å: Chain A: M.68, N.84, G.87, L.88, I.89, D.90, Y.93, Q.96, L.97, M.98 Chain B: R.141 Chain C: S.72 13 PLIP interactions: 5 interactions with chain C, 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:S.72, C:S.72, C:S.72, A:N.84, A:L.88, A:D.90, A:M.98, A:M.98, B:R.141 Water bridges: C:G.73, C:Q.119 Hydrophobic interactions: A:I.89, A:Y.93 UMP.3: 12 residues within 4Å: Chain A: S.72 Chain B: M.68, N.84, G.87, L.88, I.89, D.90, Y.93, Q.96, L.97, M.98 Chain C: R.141 13 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C, 7 interactions with chain B Hydrogen bonds: A:S.72, A:S.72, A:S.72, C:R.141, B:N.84, B:L.88, B:D.90, B:M.98, B:M.98 Water bridges: A:G.73, A:Q.119 Hydrophobic interactions: B:I.89, B:Y.93 UMP.5: 12 residues within 4Å: Chain A: R.141 Chain B: S.72 Chain C: M.68, N.84, G.87, L.88, I.89, D.90, Y.93, Q.96, L.97, M.98 13 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: C:I.89, C:Y.93 Hydrogen bonds: C:N.84, C:L.88, C:D.90, C:M.98, C:M.98, A:R.141, B:S.72, B:S.72, B:S.72 Water bridges: B:G.73, B:Q.119

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 7 residues within 4Å: Chain A: G.46, W.102, R.104 Chain B: W.102 Chain C: W.102 Ligands: TRS.4, TRS.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.103 TRS.4: 7 residues within 4Å: Chain A: W.102 Chain B: G.46, W.102, R.104 Chain C: W.102 Ligands: TRS.2, TRS.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.103 TRS.6: 7 residues within 4Å: Chain A: W.102 Chain B: W.102 Chain C: G.46, W.102, R.104 Ligands: TRS.2, TRS.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barabas, O. et al., Structural Insights into the Catalytic Mechanism of Phosphate Ester Hydrolysis by dUTPase. J.Biol.Chem. (2004)

Release Date

2004-09-07

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Deoxyuridine 5'-triphosphate nucleotidohydrolase

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