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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-hexamer

Ligands

6 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: 1 interactions with chain B, 5 interactions with chain C, 7 interactions with chain A Hydrogen bonds: B:R.141, C:S.72, C:S.72, C:S.72, A:N.84, A:L.88, A:D.90, A:M.98, A:M.98 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: 7 interactions with chain B, 1 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: B:I.89, B:Y.93 Hydrogen bonds: B:N.84, B:L.88, B:D.90, B:M.98, B:M.98, C:R.141, A:S.72, A:S.72, A:S.72 Water bridges: A:G.73, A:Q.119 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, 5 interactions with chain B, 1 interactions with chain A 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, B:S.72, B:S.72, B:S.72, A:R.141 Water bridges: B:G.73, B:Q.119 UMP.7: 12 residues within 4Å: Chain D: M.68, N.84, G.87, L.88, I.89, D.90, Y.93, Q.96, L.97, M.98 Chain E: R.141 Chain F: S.72 14 PLIP interactions: 5 interactions with chain F, 8 interactions with chain D, 1 interactions with chain E Hydrogen bonds: F:S.72, F:S.72, F:S.72, D:N.84, D:L.88, D:D.90, D:D.90, D:M.98, D:M.98, E:R.141 Water bridges: F:G.73, F:Q.119 Hydrophobic interactions: D:I.89, D:Y.93 UMP.9: 12 residues within 4Å: Chain D: S.72 Chain E: M.68, N.84, G.87, L.88, I.89, D.90, Y.93, Q.96, L.97, M.98 Chain F: R.141 14 PLIP interactions: 8 interactions with chain E, 5 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: E:I.89, E:Y.93 Hydrogen bonds: E:N.84, E:L.88, E:D.90, E:D.90, E:M.98, E:M.98, D:S.72, D:S.72, D:S.72, F:R.141 Water bridges: D:G.73, D:Q.119 UMP.11: 12 residues within 4Å: Chain D: R.141 Chain E: S.72 Chain F: M.68, N.84, G.87, L.88, I.89, D.90, Y.93, Q.96, L.97, M.98 14 PLIP interactions: 5 interactions with chain E, 8 interactions with chain F, 1 interactions with chain D Hydrogen bonds: E:S.72, E:S.72, E:S.72, F:N.84, F:L.88, F:D.90, F:D.90, F:M.98, F:M.98, D:R.141 Water bridges: E:G.73, E:Q.119 Hydrophobic interactions: F:I.89, F:Y.93

6 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 TRS.8: 7 residues within 4Å: Chain D: G.46, W.102, R.104 Chain E: W.102 Chain F: W.102 Ligands: TRS.10, TRS.12 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.103 TRS.10: 7 residues within 4Å: Chain D: W.102 Chain E: G.46, W.102, R.104 Chain F: W.102 Ligands: TRS.8, TRS.12 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.103 TRS.12: 7 residues within 4Å: Chain D: W.102 Chain E: W.102 Chain F: G.46, W.102, R.104 Ligands: TRS.8, TRS.10 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F: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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Deoxyuridine 5'-triphosphate nucleotidohydrolase

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