SMTL ID : 1slh.1 (1 other biounit)

Mycobacterium tuberculosis dUTPase complexed with magnesium and dUDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-trimer

Ligands

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

MG.1: 1 residues within 4Å: Ligands: DUD.6 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: D.48 Ligands: DUD.8 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain C: D.48, R.84 Ligands: DUD.2 No protein-ligand interaction detected (PLIP)

3 x DUD: DEOXYURIDINE-5'-DIPHOSPHATE(Non-covalent)

DUD.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.160 Chain C: R.84, S.85, G.86 Ligands: MG.7 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:Y.106 Hydrogen bonds: A:N.97, A:D.103, A:K.111, A:K.111, C:S.85, C:G.86 Water bridges: A:T.101, C:P.83 Salt bridges: C:R.84 DUD.6: 15 residues within 4Å: Chain A: R.84, S.85, G.86, Q.133 Chain B: V.81, N.97, G.100, T.101, I.102, D.103, Y.106, E.109, I.110, K.111 Ligands: MG.1 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.102, B:Y.106 Hydrogen bonds: B:N.97, B:D.103, B:Y.106, B:K.111, B:K.111, A:S.85, A:G.86, A:Q.133 Water bridges: A:R.84, A:R.84 Salt bridges: A:R.84 DUD.8: 14 residues within 4Å: 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.5 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:I.102, C:Y.106 Hydrogen bonds: C:N.97, C:D.103, C:K.111, C:K.111, B:S.85, B:G.86, B:Q.133 Salt bridges: B:R.84

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

TRS.3: 12 residues within 4Å: Chain A: L.80, H.82, P.99, Q.137 Chain B: L.80, H.82, P.99, Q.137 Chain C: L.80, H.82, P.99, Q.137 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:H.82, C:Q.137, A:H.82, A:Q.137, B:H.82 TRS.4: 11 residues within 4Å: Chain A: S.94, I.95, V.96, S.98 Chain B: S.94, I.95, V.96, L.117 Chain C: S.94, I.95, V.96 7 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:S.94, A:S.94, A:V.96, A:S.98, B:S.94, C:S.94, C:V.96

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

2004-03-16

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Deoxyuridine 5'-triphosphate nucleotidohydrolase

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