SMTL ID : 8y1q.1

Crystal structure of Aquifex aeolicus dUTPase complexed with dUMP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-trimer

Ligands

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

DU.1: 11 residues within 4Å: Chain A: V.66, N.82, G.85, T.86, I.87, D.88, Y.91, V.95, K.96 Chain C: S.70 Ligands: MG.5 30 PLIP interactions: 8 interactions with chain B, 12 interactions with chain C, 10 interactions with chain A Hydrophobic interactions: B:I.87, C:I.87, C:Y.91, A:Y.91 Hydrogen bonds: B:S.70, B:G.71, B:N.82, B:D.88, B:K.96, B:K.96, B:Q.117, C:R.69, C:S.70, C:N.82, C:D.88, C:Y.91, C:K.96, C:K.96, C:R.139, C:R.139, A:S.70, A:S.70, A:N.82, A:D.88, A:D.88, A:K.96, A:K.96, A:R.139 Salt bridges: C:R.139, A:R.139 DU.3: 11 residues within 4Å: Chain A: S.70 Chain B: N.82, G.85, T.86, I.87, D.88, Y.91, V.95, K.96 Chain C: R.139 Ligands: MG.2 Protein-ligand interaction information (PLIP) not available DU.4: 9 residues within 4Å: Chain A: R.139 Chain B: S.70 Chain C: N.82, T.86, I.87, D.88, Y.91, V.95, K.96 Protein-ligand interaction information (PLIP) not available

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

MG.2: 1 residues within 4Å: Ligands: DU.3 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: DU.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukui, K. et al., dUTP pyrophosphatases from hyperthermophilic eubacterium and archaeon: Structural and functional examinations on the suitability for PCR application. Protein Sci. (2024)

Release Date

2024-11-06

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Deoxyuridine 5'-triphosphate nucleotidohydrolase