SMTL ID : 6ljj.1

Swine dUTPase in complex with alpha,beta-iminodUTP and magnesium ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-trimer

Ligands

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

DUP.1: 22 residues within 4Å: Chain A: R.135, G.138, G.139, F.140, G.141, S.142, T.143 Chain B: P.66, R.67, S.68, G.69, Q.113 Chain C: A.80, G.81, V.82, I.83, D.84, Y.87, N.90, V.91, G.92 Ligands: MG.2 29 PLIP interactions: 10 interactions with chain C, 10 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: C:A.80, C:I.83, C:Y.87 Hydrogen bonds: C:G.81, C:V.82, C:D.84, C:G.92, C:G.92, B:R.67, B:R.67, B:S.68, B:S.68, B:S.68, B:G.69, B:Q.113, A:F.140, A:G.141, A:G.141, A:S.142, A:T.143 Water bridges: C:V.82, C:V.94, B:L.70, B:R.110, A:R.135, A:R.135, A:T.143 Salt bridges: B:R.67, A:R.135 DUP.3: 22 residues within 4Å: Chain A: A.80, G.81, V.82, I.83, D.84, Y.87, N.90, V.91, G.92 Chain B: R.135, G.138, G.139, F.140, G.141, S.142, T.143 Chain C: P.66, R.67, S.68, G.69, Q.113 Ligands: MG.4 31 PLIP interactions: 10 interactions with chain C, 12 interactions with chain A, 9 interactions with chain B Hydrogen bonds: C:R.67, C:R.67, C:S.68, C:S.68, C:S.68, C:G.69, C:Q.113, A:G.81, A:V.82, A:D.84, A:D.84, A:Y.87, A:G.92, A:G.92, B:F.140, B:G.141, B:G.141, B:S.142, B:T.143 Water bridges: C:L.70, C:R.110, A:V.82, A:V.94, B:R.135, B:R.135, B:T.143 Salt bridges: C:R.67, B:R.135 Hydrophobic interactions: A:A.80, A:I.83, A:Y.87 DUP.5: 22 residues within 4Å: Chain A: P.66, R.67, S.68, G.69, Q.113 Chain B: A.80, G.81, V.82, I.83, D.84, Y.87, N.90, V.91, G.92 Chain C: R.135, G.138, G.139, F.140, G.141, S.142, T.143 Ligands: MG.6 31 PLIP interactions: 10 interactions with chain A, 12 interactions with chain B, 9 interactions with chain C Hydrogen bonds: A:R.67, A:R.67, A:S.68, A:S.68, A:S.68, A:G.69, A:Q.113, B:G.81, B:V.82, B:D.84, B:D.84, B:Y.87, B:G.92, B:G.92, C:F.140, C:G.141, C:G.141, C:S.142, C:T.143 Water bridges: A:L.70, A:R.110, B:V.82, B:V.94, C:R.135, C:R.135, C:T.143 Salt bridges: A:R.67, C:R.135 Hydrophobic interactions: B:A.80, B:I.83, B:Y.87

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: R.135 Ligands: DUP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: R.135 Ligands: DUP.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain C: R.135 Ligands: DUP.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liang, R. et al., Structural comparisons of host and African swine fever virus dUTPases reveal new clues for inhibitor development. J.Biol.Chem. (2020)

Release Date

2020-11-11

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial isoform 1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial isoform 1