SMTL ID : 8y1w.1

Crystal structure of Thermococcus pacificus dUTPase complexed with dUMP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: K.46, E.47, G.48 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.47

1 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.2: 11 residues within 4Å: Chain A: M.76, F.91, A.92, W.93, V.94, D.95, W.98, L.102, T.103, L.104, Y.138 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.92, A:V.94, A:W.98, A:L.102 Hydrogen bonds: A:A.92, A:W.93, A:D.95, A:T.103, A:T.103, A:Y.138, A:Y.138

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 2 residues within 4Å: Chain A: Y.36, G.39 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.39 PO4.4: 1 residues within 4Å: Chain A: R.121 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.121

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

dCTP deaminase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

dCTP deaminase