SMTL ID : 3loj.1

Structure of Mycobacterium tuberculosis dUTPase H145A mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-trimer

Ligands

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

DUP.1: 21 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, A.165, G.166, S.167, S.168 Chain C: R.84, S.85, G.86, Q.133 Ligands: MG.5, MN.6 26 PLIP interactions: 7 interactions with chain B, 10 interactions with chain C, 9 interactions with chain A Hydrogen bonds: B:A.165, B:G.166, B:S.167, B:S.168, B:G.169, C:R.84, C:R.84, C:S.85, C:S.85, C:S.85, C:G.86, C:Q.133, A:N.97, A:T.101, A:D.103, A:K.111, A:K.111 Water bridges: B:S.168, C:L.87, C:R.130, A:T.101, A:Y.106, A:Y.106 Salt bridges: B:R.160, C:R.84 Hydrophobic interactions: A:Y.106 DUP.7: 21 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, A.165, G.166, S.167, S.168 Ligands: MG.11, MN.12 26 PLIP interactions: 9 interactions with chain B, 10 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: B:Y.106 Hydrogen bonds: B:N.97, B:T.101, B:D.103, B:K.111, B:K.111, A:R.84, A:R.84, A:S.85, A:S.85, A:S.85, A:G.86, A:Q.133, C:A.165, C:G.166, C:S.167, C:S.168, C:G.169 Water bridges: B:T.101, B:Y.106, B:Y.106, A:L.87, A:R.130, C:S.168 Salt bridges: A:R.84, C:R.160 DUP.13: 21 residues within 4Å: Chain A: R.160, G.164, A.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.17, MN.18 26 PLIP interactions: 10 interactions with chain B, 7 interactions with chain A, 9 interactions with chain C Hydrogen bonds: B:R.84, B:R.84, B:S.85, B:S.85, B:S.85, B:G.86, B:Q.133, A:A.165, A:G.166, A:S.167, A:S.168, A:G.169, C:N.97, C:T.101, C:D.103, C:K.111, C:K.111 Water bridges: B:L.87, B:R.130, A:S.168, C:T.101, C:Y.106, C:Y.106 Salt bridges: B:R.84, A:R.160 Hydrophobic interactions: C:Y.106

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: S.149, F.150, D.151 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.150, A:D.151 Water bridges: A:S.148 GOL.3: 4 residues within 4Å: Chain A: P.35, Y.50, R.130 Chain C: G.170 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Water bridges: C:G.170 Hydrogen bonds: A:Y.50, A:R.130 GOL.8: 3 residues within 4Å: Chain B: S.149, F.150, D.151 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.150, B:D.151 Water bridges: B:S.148 GOL.9: 4 residues within 4Å: Chain A: G.170 Chain B: P.35, Y.50, R.130 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.50, B:R.130 Water bridges: A:G.170 GOL.14: 3 residues within 4Å: Chain C: S.149, F.150, D.151 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.150, C:D.151 Water bridges: C:S.148 GOL.15: 4 residues within 4Å: Chain B: G.170 Chain C: P.35, Y.50, R.130 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Y.50, C:R.130 Water bridges: B:G.170

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

TRS.4: 7 residues within 4Å: Chain A: S.94, L.117 Chain B: S.94, I.95, V.96 Ligands: TRS.10, TRS.16 8 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:S.94, B:I.95, A:S.94 Water bridges: B:S.94, B:I.95, B:S.98, A:I.95, C:S.94 TRS.10: 7 residues within 4Å: Chain B: S.94, L.117 Chain C: S.94, I.95, V.96 Ligands: TRS.4, TRS.16 8 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:S.94, C:I.95, B:S.94 Water bridges: C:S.94, C:S.98, A:S.94, A:I.95, A:I.95 TRS.16: 7 residues within 4Å: Chain A: S.94, I.95, V.96 Chain C: S.94, L.117 Ligands: TRS.4, TRS.10 8 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A, 1 interactions with chain C Water bridges: B:S.94, B:I.95, A:S.94, A:I.95, A:S.98 Hydrogen bonds: A:S.94, A:I.95, C:S.94

3 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain B: R.160 Ligands: DUP.1, MN.6 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain C: R.160 Ligands: DUP.7, MN.12 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain A: R.160 Ligands: DUP.13, MN.18 No protein-ligand interaction detected (PLIP)

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.6: 3 residues within 4Å: Chain B: R.160 Ligands: DUP.1, MG.5 No protein-ligand interaction detected (PLIP) MN.12: 3 residues within 4Å: Chain C: R.160 Ligands: DUP.7, MG.11 No protein-ligand interaction detected (PLIP) MN.18: 3 residues within 4Å: Chain A: R.160 Ligands: DUP.13, MG.17 No protein-ligand interaction detected (PLIP)

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

2010-08-11

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Deoxyuridine 5'-triphosphate nucleotidohydrolase