SMTL ID : 8qld.1

Bacteriophage T5 dUTPase mutant with loop deletion (30-35 aa)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: K.14, R.26, R.106 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.106 Salt bridges: A:R.26, A:R.106 SO4.2: 4 residues within 4Å: Chain A: R.62, S.63, S.64, Q.109 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.24, A:S.63, A:S.63, A:S.64, A:R.106 Water bridges: A:Q.109 Salt bridges: A:R.62 SO4.5: 3 residues within 4Å: Chain B: K.14, R.26, R.106 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.106 Salt bridges: B:K.14, B:R.26, B:R.106 SO4.8: 3 residues within 4Å: Chain C: K.14, R.26, R.106 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:K.14, C:R.26, C:R.106

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: I.79, Y.83, I.87, K.88 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain B: R.62, S.63, S.64, Q.109 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.62, B:S.63, B:S.64, B:S.64 Water bridges: B:Q.109, B:Q.109 GOL.6: 4 residues within 4Å: Chain C: R.62, S.63, S.64, Q.109 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.62, C:S.63, C:S.64, C:S.64, C:Q.109 Water bridges: C:S.63, C:S.63, A:N.74 GOL.7: 3 residues within 4Å: Chain C: M.98, Q.99, T.100 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:M.98, C:Q.99, C:T.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Glukhov, A. et al., Bacteriophage T5 dUTPase: Combination of Common Enzymatic and Novel Functions. Int J Mol Sci (2024)

Release Date

2024-01-17

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Deoxyuridine 5'-triphosphate nucleotidohydrolase