SMTL ID : 3p48.1

Structure of the yeast dUTPase DUT1 in complex with dUMPNPP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-trimer

Ligands

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

DUP.1: 15 residues within 4Å: Chain A: P.67, R.68, S.69, G.70, Q.114 Chain C: A.81, G.82, V.83, V.84, D.85, Y.88, E.91, V.92, K.93 Ligands: MG.2 17 PLIP interactions: 9 interactions with chain C, 8 interactions with chain A Hydrophobic interactions: C:A.81, C:Y.88 Hydrogen bonds: C:G.82, C:V.83, C:D.85, C:K.93, C:K.93, A:R.68, A:S.69, A:S.69, A:G.70, A:Q.114 Water bridges: C:V.83, C:V.95, A:L.71, A:R.111, A:R.111 DUP.3: 14 residues within 4Å: Chain A: A.81, G.82, V.83, V.84, D.85, Y.88, V.92, K.93 Chain B: P.67, R.68, S.69, G.70, Q.114 Ligands: MG.5 17 PLIP interactions: 8 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:R.68, B:S.69, B:S.69, B:G.70, B:Q.114, A:G.82, A:V.83, A:D.85, A:K.93, A:K.93 Water bridges: B:R.68, B:L.71, B:R.111, A:D.85, A:V.95 Hydrophobic interactions: A:A.81, A:Y.88 DUP.4: 15 residues within 4Å: Chain B: G.80, A.81, G.82, V.83, V.84, D.85, Y.88, E.91, V.92, K.93 Chain C: R.68, S.69, G.70, Q.114 Ligands: MG.6 16 PLIP interactions: 9 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:A.81, B:V.84, B:Y.88 Hydrogen bonds: B:G.82, B:V.83, B:D.85, B:D.85, B:K.93, B:K.93, C:P.67, C:R.68, C:S.69, C:G.70, C:Q.114 Water bridges: C:S.69, C:S.69

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

MG.2: 1 residues within 4Å: Ligands: DUP.1 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: DUP.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain C: D.32 Ligands: DUP.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tchigvintsev, A. et al., Structure and activity of the Saccharomyces cerevisiae dUTP pyrophosphatase DUT1, an essential housekeeping enzyme. Biochem.J. (2011)

Release Date

2010-10-27

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Deoxyuridine 5'-triphosphate nucleotidohydrolase