SMTL ID : 6hde.1

Structure of Escherichia coli dUTPase Q93H mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 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.71, S.72, G.73, Q.119 Chain B: M.68, N.84, G.87, L.88, I.89, D.90, Y.93, Q.96, L.97, M.98 Ligands: MG.3 22 PLIP interactions: 9 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:I.89, B:Y.93 Hydrogen bonds: B:N.84, B:L.88, B:D.90, B:M.98, B:M.98, A:R.71, A:R.71, A:S.72, A:S.72, A:G.73, A:Q.119, A:Q.119 Water bridges: B:Y.93, B:Y.93, A:D.32, A:R.71, A:R.71, A:L.74, A:R.116 Salt bridges: A:R.71 DUP.2: 20 residues within 4Å: Chain A: R.141, G.144, G.145, F.146, G.147, H.148, S.149 Chain B: R.71, S.72, G.73, Q.119 Chain C: M.68, N.84, G.87, L.88, I.89, D.90, Y.93, M.98 Ligands: MG.5 27 PLIP interactions: 7 interactions with chain C, 11 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: C:I.89, C:Y.93 Hydrogen bonds: C:N.84, C:L.88, C:D.90, C:M.98, C:M.98, B:R.71, B:S.72, B:S.72, B:S.72, B:G.73, B:Q.119, B:Q.119, A:G.145, A:F.146, A:G.147, A:H.148, A:S.149 Water bridges: B:L.74, B:R.116, B:R.116, A:R.141, A:R.141 Salt bridges: B:R.71, A:R.141, A:H.148 DUP.4: 21 residues within 4Å: Chain A: M.68, N.84, G.87, L.88, I.89, D.90, Y.93, Q.96, M.98 Chain B: R.141, G.144, G.145, F.146, G.147, H.148, S.149 Chain C: R.71, S.72, G.73, Q.119 Ligands: MG.6 26 PLIP interactions: 11 interactions with chain B, 9 interactions with chain C, 6 interactions with chain A Hydrogen bonds: B:G.145, B:F.146, B:G.147, B:H.148, B:S.149, B:S.149, C:R.71, C:S.72, C:S.72, C:S.72, C:G.73, C:Q.119, A:N.84, A:L.88, A:D.90, A:M.98, A:M.98 Water bridges: B:R.141, B:R.141, B:S.149, C:L.74, C:R.116 Salt bridges: B:R.141, B:H.148, C:R.71 Hydrophobic interactions: A:Y.93

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

MG.3: 1 residues within 4Å: Ligands: DUP.1 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: DUP.2 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: DUP.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benedek, A. et al., The Role of a Key Amino Acid Position in Species-Specific Proteinaceous dUTPase Inhibition. Biomolecules (2019)

Release Date

2019-08-28

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Deoxyuridine 5'-triphosphate nucleotidohydrolase