SMTL ID : 2hr6.1

Crystal structure of dUTPase in complex with substrate analogue dUDP and manganese

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-trimer

Ligands

3 x MN: MANGANESE (II) ION(Non-functional Binders)

MN.1: 1 residues within 4Å: Ligands: DUD.2 No protein-ligand interaction detected (PLIP) MN.4: 1 residues within 4Å: Ligands: DUD.5 No protein-ligand interaction detected (PLIP) MN.7: 1 residues within 4Å: Ligands: DUD.8 No protein-ligand interaction detected (PLIP)

3 x DUD: DEOXYURIDINE-5'-DIPHOSPHATE(Non-covalent)

DUD.2: 15 residues within 4Å: Chain A: M.68, N.84, G.87, L.88, I.89, D.90, Y.93, Q.96, L.97, M.98 Chain C: R.71, S.72, G.73, Q.119 Ligands: MN.1 17 PLIP interactions: 8 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:I.89, A:Y.93 Hydrogen bonds: A:N.84, A:L.88, A:D.90, A:M.98, A:M.98, C:S.72, C:G.73, C:Q.119, C:Q.119 Water bridges: A:S.100, C:R.71, C:S.72, C:S.72, C:L.74 Salt bridges: C:R.71 DUD.5: 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: MN.4 17 PLIP interactions: 9 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:S.72, A:G.73, A:Q.119, A:Q.119, B:N.84, B:L.88, B:D.90, B:M.98, B:M.98 Water bridges: A:R.71, A:S.72, A:S.72, A:L.74, B:S.100 Salt bridges: A:R.71 Hydrophobic interactions: B:I.89, B:Y.93 DUD.8: 15 residues within 4Å: 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, Q.96, L.97, M.98 Ligands: MN.7 17 PLIP interactions: 8 interactions with chain C, 9 interactions with chain B 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:S.72, B:G.73, B:Q.119, B:Q.119 Water bridges: C:S.100, B:R.71, B:S.72, B:S.72, B:L.74 Salt bridges: B:R.71

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 2 residues within 4Å: Chain A: K.3, K.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.3, A:K.3, A:K.4 EDO.6: 2 residues within 4Å: Chain B: K.3, K.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.3, B:K.3, B:K.4 EDO.9: 2 residues within 4Å: Chain C: K.3, K.4 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.3, C:K.3, C:K.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kovari, J. et al., Methylene substitution at the alpha-beta bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site. Proteins (2008)

Release Date

2007-07-31

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Deoxyuridine 5'-triphosphate nucleotidohydrolase

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