SMTL ID : 3h6d.1 (1 other biounit)

Structure of the mycobacterium tuberculosis DUTPase D28N 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.2 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: DUP.6 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: DUP.10 No protein-ligand interaction detected (PLIP)

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

DUP.2: 15 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 Chain C: R.160 Ligands: MG.1 19 PLIP interactions: 9 interactions with chain A, 9 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:Y.106 Hydrogen bonds: A:N.97, A:T.101, A:T.101, A:D.103, A:D.103, A:Y.106, A:K.111, A:K.111, B:R.84, B:S.85, B:S.85, B:S.85, B:G.86, B:Q.133 Water bridges: B:R.84, B:L.87 Salt bridges: B:R.84, C:R.160 DUP.6: 15 residues within 4Å: Chain A: R.160 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.5 19 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: B:Y.106 Hydrogen bonds: B:N.97, B:T.101, B:T.101, B:D.103, B:D.103, B:Y.106, B:K.111, B:K.111, C:R.84, C:S.85, C:S.85, C:S.85, C:G.86, C:Q.133 Salt bridges: A:R.160, C:R.84 Water bridges: C:R.84, C:L.87 DUP.10: 15 residues within 4Å: Chain A: R.84, S.85, G.86, Q.133 Chain B: R.160 Chain C: N.97, G.100, T.101, I.102, D.103, Y.106, E.109, I.110, K.111 Ligands: MG.9 19 PLIP interactions: 9 interactions with chain A, 9 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:R.84, A:S.85, A:S.85, A:S.85, A:G.86, A:Q.133, C:N.97, C:T.101, C:T.101, C:D.103, C:D.103, C:Y.106, C:K.111, C:K.111 Water bridges: A:R.84, A:L.87 Salt bridges: A:R.84, B:R.160 Hydrophobic interactions: C:Y.106

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

TRS.3: 13 residues within 4Å: Chain A: S.94, I.95, V.96 Chain B: S.94, I.95, V.96, L.117 Chain C: S.94, I.95, V.96, L.117 Ligands: TRS.7, TRS.11 9 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C, 3 interactions with chain B Hydrogen bonds: A:S.94, A:I.95, C:S.94, C:I.95, B:S.94 Water bridges: A:S.98, C:S.98, B:S.98, B:S.98 TRS.4: 2 residues within 4Å: Chain A: R.29, P.32 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.29 Water bridges: A:R.29, A:R.29 TRS.7: 13 residues within 4Å: Chain A: S.94, I.95, V.96, L.117 Chain B: S.94, I.95, V.96 Chain C: S.94, I.95, V.96, L.117 Ligands: TRS.3, TRS.11 8 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B, 3 interactions with chain C Hydrogen bonds: A:S.94, B:S.94, B:I.95, C:S.94 Water bridges: A:S.98, B:S.98, C:S.98, C:S.98 TRS.8: 2 residues within 4Å: Chain B: R.29, P.32 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.29 Water bridges: B:R.29, B:R.29 TRS.11: 13 residues within 4Å: Chain A: S.94, I.95, V.96, L.117 Chain B: S.94, I.95, V.96, L.117 Chain C: S.94, I.95, V.96 Ligands: TRS.3, TRS.7 9 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B, 3 interactions with chain C Hydrogen bonds: A:S.94, B:S.94, B:I.95, C:S.94, C:I.95 Water bridges: A:S.98, A:S.98, B:S.98, C:S.98 TRS.12: 2 residues within 4Å: Chain C: R.29, P.32 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.29 Water bridges: C:R.29, C:R.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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

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