SMTL ID : 5f9k.1

Dictyostelium discoideum dUTPase at 2.2 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 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: R.64, S.65, G.66, L.67, Q.110 Chain C: I.61, G.76, A.77, G.78, V.79, I.80, D.81, Y.84, G.89, V.91 18 PLIP interactions: 8 interactions with chain A, 10 interactions with chain C Hydrogen bonds: A:R.64, A:R.64, A:S.65, A:S.65, A:G.66, A:L.67, A:Q.110, C:G.78, C:V.79, C:D.81, C:D.81, C:Y.84, C:G.89, C:G.89 Salt bridges: A:R.64 Hydrophobic interactions: C:A.77, C:I.80, C:Y.84 DUP.2: 8 residues within 4Å: Chain A: Y.84, G.89, V.91 Chain B: R.64, S.65, G.66, R.107 Ligands: MG.4 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.65, B:S.65, B:G.66, B:L.67, A:Y.84, A:Y.84 Salt bridges: B:R.64, B:R.107 Hydrophobic interactions: A:V.91 DUP.9: 15 residues within 4Å: Chain B: A.77, G.78, V.79, I.80, D.81, Y.84, N.87, V.88, G.89, V.91 Chain C: R.64, S.65, G.66, Q.110 Ligands: MG.3 12 PLIP interactions: 3 interactions with chain C, 9 interactions with chain B Hydrogen bonds: C:S.65, C:G.66, B:G.78, B:D.81, B:D.81, B:G.89, B:G.89 Salt bridges: C:R.64 Hydrophobic interactions: B:A.77, B:I.80, B:Y.84 Water bridges: B:V.91

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain B: V.79, D.81 Chain C: Q.110 Ligands: DUP.9 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.81 MG.4: 4 residues within 4Å: Chain B: R.64, S.65, Q.110 Ligands: DUP.2 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain B: R.60, I.61, A.77 Ligands: MG.7 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:I.61, H2O.3, H2O.4 MG.6: 2 residues within 4Å: Chain B: D.74 Ligands: MG.7 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain C: R.60, P.63 Ligands: MG.5, MG.6 No protein-ligand interaction detected (PLIP)

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chia, C.P. et al., Mitochondrial localization of Dictyostelium discoideum dUTPase mediated by its N-terminus. Bmc Res Notes (2020)

Release Date

2016-12-14

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Deoxyuridine 5'-triphosphate nucleotidohydrolase