SMTL ID : 1sjn.1

Mycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

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

MG.1: 2 residues within 4Å: Chain C: R.140 Ligands: DUP.7 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: DUP.6 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain B: R.140 Ligands: DUP.2 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.77, G.80, T.81, I.82, D.83, Y.86, E.89, I.90, K.91 Chain B: R.140 Chain C: R.64, S.65, G.66, Q.113 Ligands: MG.8 20 PLIP interactions: 7 interactions with chain A, 10 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: A:Y.86 Hydrogen bonds: A:N.77, A:D.83, A:Y.86, A:K.91, A:K.91, C:R.64, C:R.64, C:S.65, C:S.65, C:G.66, C:Q.113 Water bridges: A:T.81, C:L.67, C:R.110, C:R.110, C:Q.113, B:R.140, B:R.140 Salt bridges: B:R.140 DUP.6: 15 residues within 4Å: Chain B: R.64, S.65, G.66, Q.113 Chain C: N.77, G.80, T.81, I.82, D.83, Y.86, E.89, I.90, K.91 Ligands: MG.4, NO3.5 16 PLIP interactions: 8 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:R.64, B:S.65, B:S.65, B:G.66, B:Q.113, C:N.77, C:D.83, C:D.83, C:Y.86, C:K.91, C:K.91 Water bridges: B:R.110, B:R.110, B:Q.113, C:T.81 Hydrophobic interactions: C:Y.86 DUP.7: 18 residues within 4Å: Chain A: R.64, S.65, G.66, Q.113 Chain B: N.77, G.80, T.81, I.82, D.83, Y.86, E.89, I.90, K.91 Chain C: R.140, G.143, G.144, H.145 Ligands: MG.1 21 PLIP interactions: 3 interactions with chain C, 10 interactions with chain A, 8 interactions with chain B Hydrogen bonds: C:R.140, C:H.145, A:R.64, A:S.65, A:S.65, A:G.66, A:Q.113, B:N.77, B:T.81, B:D.83, B:D.83, B:K.91, B:K.91 Salt bridges: C:R.140 Water bridges: A:R.64, A:L.67, A:R.110, A:R.110, A:Q.113 Hydrophobic interactions: B:I.82, B:Y.86

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

TRS.3: 12 residues within 4Å: Chain A: S.74, I.75, V.76, L.97 Chain B: S.74, I.75, V.76, L.97 Chain C: S.74, I.75, V.76, L.97 11 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A, 4 interactions with chain C Hydrogen bonds: B:S.74, B:I.75, A:S.74, A:I.75, C:S.74, C:I.75 Water bridges: B:S.78, A:S.74, A:I.75, C:S.74, C:S.78

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.5: 5 residues within 4Å: Chain B: R.64, G.66, L.67, R.70 Ligands: DUP.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.64, B:R.70, B:R.70 Water bridges: B:G.66, B:L.67 NO3.9: 4 residues within 4Å: Chain A: F.130, D.131 Chain C: A.52, R.87 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.87, C:R.87, A:D.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chan, S. et al., Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism. J.Mol.Biol. (2004)

Release Date

2004-03-09

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Deoxyuridine 5'-triphosphate nucleotidohydrolase