SMTL ID : 1rn8.1

Crystal structure of dUTPase complexed with substrate analogue imido-dUTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-trimer

Ligands

3 x MG: MAGNESIUM ION(Non-functional Binders)

MG.1: 1 residues within 4Å: Ligands: DUP.3 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: DUP.7 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: DUP.11 No protein-ligand interaction detected (PLIP)

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 2 residues within 4Å: Chain A: Q.112, E.115 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.112, A:E.115 Water bridges: A:R.34, A:R.34, A:E.115, A:E.115, A:R.116 ACT.6: 2 residues within 4Å: Chain B: Q.112, E.115 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Q.112, B:E.115 Water bridges: B:R.34, B:R.34, B:E.115, B:E.115, B:R.116 ACT.10: 2 residues within 4Å: Chain C: Q.112, E.115 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Q.112, C:E.115 Water bridges: C:R.34, C:R.34, C:E.115, C:E.115, C:R.116

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

DUP.3: 16 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: F.146 Chain C: R.71, S.72, G.73, Q.119 Ligands: MG.1 20 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: A:I.89, A:Y.93 Hydrogen bonds: A:N.84, A:L.88, A:D.90, A:M.98, A:M.98, C:R.71, C:S.72, C:S.72, C:G.73, C:Q.119, C:Q.119 Water bridges: B:Q.152, B:Q.152, B:Q.152, B:Q.152, C:R.71, C:R.116 pi-Stacking: B:F.146 DUP.7: 16 residues within 4Å: Chain A: R.71, S.72, G.73, Q.119 Chain B: M.68, N.84, G.87, L.88, I.89, D.90, Y.93, Q.96, L.97, M.98 Chain C: F.146 Ligands: MG.5 20 PLIP interactions: 8 interactions with chain A, 7 interactions with chain B, 5 interactions with chain C Hydrogen bonds: A:R.71, A:S.72, A:S.72, A:G.73, A:Q.119, A:Q.119, B:N.84, B:L.88, B:D.90, B:M.98, B:M.98 Water bridges: A:R.71, A:R.116, C:Q.152, C:Q.152, C:Q.152, C:Q.152 Hydrophobic interactions: B:I.89, B:Y.93 pi-Stacking: C:F.146 DUP.11: 16 residues within 4Å: Chain A: F.146 Chain B: R.71, S.72, G.73, Q.119 Chain C: M.68, N.84, G.87, L.88, I.89, D.90, Y.93, Q.96, L.97, M.98 Ligands: MG.9 20 PLIP interactions: 5 interactions with chain A, 7 interactions with chain C, 8 interactions with chain B Water bridges: A:Q.152, A:Q.152, A:Q.152, A:Q.152, B:R.71, B:R.116 pi-Stacking: A:F.146 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:R.71, B:S.72, B:S.72, B:G.73, B:Q.119, B:Q.119

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

TRS.4: 6 residues within 4Å: Chain A: W.102, R.104 Chain B: W.102 Chain C: W.102 Ligands: TRS.8, TRS.12 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Water bridges: C:W.102, B:R.104 Hydrogen bonds: A:R.104 TRS.8: 6 residues within 4Å: Chain A: W.102 Chain B: W.102, R.104 Chain C: W.102 Ligands: TRS.4, TRS.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.104 TRS.12: 6 residues within 4Å: Chain A: W.102 Chain B: W.102 Chain C: W.102, R.104 Ligands: TRS.4, TRS.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.104

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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