SMTL ID : 3i93.1

Crystal structure of Mycobacterium tuberculosis dUTPase STOP138T mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

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

MG.1: 1 residues within 4Å: Ligands: DUP.10 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: DUP.2 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: DUP.6 No protein-ligand interaction detected (PLIP)

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

DUP.2: 14 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.84, S.85, G.86, Q.133 Ligands: MG.5 18 PLIP interactions: 11 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:R.84, B:S.85, B:S.85, B:G.86, B:Q.133, A:N.97, A:D.103, A:D.103, A:Y.106, A:K.111, A:K.111 Water bridges: B:D.44, B:D.48, B:R.84, B:R.130, B:R.130 Salt bridges: B:R.84 Hydrophobic interactions: A:Y.106 DUP.6: 14 residues within 4Å: Chain B: N.97, G.100, T.101, I.102, D.103, Y.106, E.109, I.110, K.111 Chain C: R.84, S.85, G.86, Q.133 Ligands: MG.9 18 PLIP interactions: 11 interactions with chain C, 7 interactions with chain B Hydrogen bonds: C:R.84, C:S.85, C:S.85, C:G.86, C:Q.133, B:N.97, B:D.103, B:D.103, B:Y.106, B:K.111, B:K.111 Water bridges: C:D.44, C:D.48, C:R.84, C:R.130, C:R.130 Salt bridges: C:R.84 Hydrophobic interactions: B:Y.106 DUP.10: 14 residues within 4Å: Chain A: 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.1 18 PLIP interactions: 11 interactions with chain A, 7 interactions with chain C Hydrogen bonds: A:R.84, A:S.85, A:S.85, A:G.86, A:Q.133, C:N.97, C:D.103, C:D.103, C:Y.106, C:K.111, C:K.111 Water bridges: A:D.44, A:D.48, A:R.84, A:R.130, A:R.130 Salt bridges: A:R.84 Hydrophobic interactions: C:Y.106

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

TRS.3: 9 residues within 4Å: Chain A: S.94, I.95, V.96, L.117 Chain B: S.94, I.95, L.117 Ligands: TRS.7, TRS.11 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.94, A:S.94 Water bridges: B:S.98, A:S.98 TRS.4: 2 residues within 4Å: Chain A: R.29, P.32 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Water bridges: C:E.146, C:E.146, A:R.29 TRS.7: 9 residues within 4Å: Chain B: S.94, I.95, V.96, L.117 Chain C: S.94, I.95, L.117 Ligands: TRS.3, TRS.11 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.94, C:S.94 Water bridges: B:S.98, C:S.98 TRS.8: 2 residues within 4Å: Chain B: R.29, P.32 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:E.146, A:E.146, B:R.29 TRS.11: 9 residues within 4Å: Chain A: S.94, I.95, L.117 Chain C: S.94, I.95, V.96, L.117 Ligands: TRS.3, TRS.7 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:S.94, C:S.94 Water bridges: A:S.98, C:S.98 TRS.12: 2 residues within 4Å: Chain C: R.29, P.32 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Water bridges: B:E.146, B:E.146, C:R.29

Links

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Citation

Takacs, E. et al., Direct contacts between conserved motifs of different subunits provide major contribution to active site organization in human and mycobacterial dUTPases. Febs Lett. (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