SMTL ID : 3hza.1

Crystal structure of dUTPase H145W mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-trimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain B: R.160 Ligands: DUP.2 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain C: R.160 Ligands: DUP.7 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain A: R.160 Ligands: DUP.12 No protein-ligand interaction detected (PLIP)

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

DUP.2: 20 residues within 4Å: Chain A: N.97, G.100, T.101, I.102, D.103, Y.106, E.109, I.110, K.111 Chain B: R.160, G.164, W.165, G.166, S.167, S.168 Chain C: R.84, S.85, G.86, Q.133 Ligands: MG.1 23 PLIP interactions: 7 interactions with chain A, 9 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: A:Y.106 Hydrogen bonds: A:N.97, A:T.101, A:D.103, A:K.111, A:K.111, C:R.84, C:R.84, C:S.85, C:S.85, C:S.85, C:G.86, C:Q.133, B:W.165, B:G.166, B:S.167, B:S.168 Water bridges: A:T.101, C:L.87, B:S.168, B:S.168 Salt bridges: C:R.84, B:R.160 DUP.7: 20 residues within 4Å: Chain A: R.84, S.85, G.86, Q.133 Chain B: N.97, G.100, T.101, I.102, D.103, Y.106, E.109, I.110, K.111 Chain C: R.160, G.164, W.165, G.166, S.167, S.168 Ligands: MG.6 23 PLIP interactions: 7 interactions with chain B, 7 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: B:Y.106 Hydrogen bonds: B:N.97, B:T.101, B:D.103, B:K.111, B:K.111, C:W.165, C:G.166, C:S.167, C:S.168, A:R.84, A:R.84, A:S.85, A:S.85, A:S.85, A:G.86, A:Q.133 Water bridges: B:T.101, C:S.168, C:S.168, A:L.87 Salt bridges: C:R.160, A:R.84 DUP.12: 20 residues within 4Å: Chain A: R.160, G.164, W.165, G.166, S.167, S.168 Chain B: R.84, S.85, G.86, Q.133 Chain C: N.97, G.100, T.101, I.102, D.103, Y.106, E.109, I.110, K.111 Ligands: MG.11 23 PLIP interactions: 7 interactions with chain A, 7 interactions with chain C, 9 interactions with chain B Hydrogen bonds: A:W.165, A:G.166, A:S.167, A:S.168, C:N.97, C:T.101, C:D.103, C:K.111, C:K.111, B:R.84, B:R.84, B:S.85, B:S.85, B:S.85, B:G.86, B:Q.133 Water bridges: A:S.168, A:S.168, C:T.101, B:L.87 Salt bridges: A:R.160, B:R.84 Hydrophobic interactions: C:Y.106

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: A.153, L.155 Chain C: A.26 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:A.153 Water bridges: C:T.24 GOL.4: 1 residues within 4Å: Chain A: D.151 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.151 GOL.8: 3 residues within 4Å: Chain A: A.26 Chain B: A.153, L.155 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:T.24 Hydrogen bonds: B:A.153 GOL.9: 1 residues within 4Å: Chain B: D.151 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.151 GOL.13: 3 residues within 4Å: Chain B: A.26 Chain C: A.153, L.155 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:A.153 Water bridges: B:T.24 GOL.14: 1 residues within 4Å: Chain C: D.151 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.151

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 7 residues within 4Å: Chain A: S.94, L.117 Chain B: S.94, I.95, V.96 Ligands: TRS.10, TRS.15 8 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:S.94, B:S.94, B:I.95 Water bridges: A:I.95, B:S.94, B:S.98, C:S.94, C:I.95 TRS.10: 7 residues within 4Å: Chain B: S.94, L.117 Chain C: S.94, I.95, V.96 Ligands: TRS.5, TRS.15 7 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 3 interactions with chain C Water bridges: A:S.94, A:I.95, B:I.95, C:S.94 Hydrogen bonds: B:S.94, C:S.94, C:I.95 TRS.15: 7 residues within 4Å: Chain A: S.94, I.95, V.96 Chain C: S.94, L.117 Ligands: TRS.5, TRS.10 8 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:S.94, A:I.95, C:S.94 Water bridges: A:S.94, A:S.98, B:S.94, B:I.95, C:I.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pecsi, I. et al., Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase. Nucleic Acids Res. (2010)

Release Date

2009-11-24

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Deoxyuridine 5'-triphosphate nucleotidohydrolase