SMTL ID : 1six.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-trimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain C: R.160 Ligands: DUP.2 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: R.160 Ligands: DUP.5 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: R.160 Ligands: DUP.8 No protein-ligand interaction detected (PLIP)

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

DUP.2: 17 residues within 4Å: Chain A: H.41, 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 Ligands: MG.1 22 PLIP interactions: 7 interactions with chain B, 12 interactions with chain A, 3 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:S.85, A:S.85, A:G.86, A:Q.133, C:R.160, C:G.164 Water bridges: B:T.101, A:R.84, A:L.87, A:R.90, A:R.130, A:R.130, A:Q.133 Salt bridges: A:H.41, C:R.160 DUP.5: 17 residues within 4Å: Chain A: R.160, G.164 Chain B: H.41, 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.4 22 PLIP interactions: 12 interactions with chain B, 7 interactions with chain C, 3 interactions with chain A Hydrogen bonds: B:R.84, B:S.85, B:S.85, B:G.86, B:Q.133, C:N.97, C:T.101, C:D.103, C:K.111, C:K.111, A:R.160, A:G.164 Water bridges: B:R.84, B:L.87, B:R.90, B:R.130, B:R.130, B:Q.133, C:T.101 Salt bridges: B:H.41, A:R.160 Hydrophobic interactions: C:Y.106 DUP.8: 17 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 Chain C: H.41, R.84, S.85, G.86, Q.133 Ligands: MG.7 22 PLIP interactions: 12 interactions with chain C, 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: C:R.84, 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, B:R.160, B:G.164 Water bridges: C:R.84, C:L.87, C:R.90, C:R.130, C:R.130, C:Q.133, A:T.101 Salt bridges: C:H.41, B:R.160 Hydrophobic interactions: A:Y.106

3 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, L.117 Chain B: S.94, I.95, V.96, L.117 Chain C: S.94, I.95, V.96 Ligands: TRS.6, TRS.9 9 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B, 3 interactions with chain C Hydrogen bonds: A:S.94, A:I.95, B:S.94, C:S.94 Water bridges: A:I.95, B:S.94, B:S.98, C:S.94, C:S.98 TRS.6: 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.3, TRS.9 9 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A, 3 interactions with chain C Hydrogen bonds: B:S.94, B:I.95, A:S.94, C:S.94 Water bridges: B:S.98, A:S.94, A:I.95, C:S.94, C:S.98 TRS.9: 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.6 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, C:S.94, C:I.95 Water bridges: A:S.94, A:S.98, B:S.94, B:S.98, C:S.98

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
A

C
A

Deoxyuridine 5'-triphosphate nucleotidohydrolase

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