SMTL ID : 2py4.1

Full length structure of the Mycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 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: 20 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, G.164, H.165, G.166, S.167, S.168 Ligands: MG.1 27 PLIP interactions: 10 interactions with chain B, 6 interactions with chain C, 11 interactions with chain A Hydrogen bonds: B:R.84, B:R.84, B:S.85, B:S.85, B:S.85, B:G.86, B:Q.133, C:H.165, C:G.166, C:S.167, C:S.168, A:N.97, A:T.101, A:D.103, A:D.103, A:Y.106, A:K.111, A:K.111 Water bridges: B:L.87, B:R.130, C:S.168, A:T.101, A:A.113, A:A.113 Salt bridges: B:R.84, C:R.160 Hydrophobic interactions: A:Y.106 DUP.5: 20 residues within 4Å: Chain A: R.160, G.164, H.165, G.166, S.167, S.168 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.4 27 PLIP interactions: 6 interactions with chain A, 10 interactions with chain C, 11 interactions with chain B Hydrogen bonds: A:H.165, A:G.166, A:S.167, A:S.168, C:R.84, C:R.84, C:S.85, C:S.85, C:S.85, C:G.86, C:Q.133, B:N.97, B:T.101, B:D.103, B:D.103, B:Y.106, B:K.111, B:K.111 Water bridges: A:S.168, C:L.87, C:R.130, B:T.101, B:A.113, B:A.113 Salt bridges: A:R.160, C:R.84 Hydrophobic interactions: B:Y.106 DUP.8: 20 residues within 4Å: Chain A: R.84, S.85, G.86, Q.133 Chain B: R.160, G.164, H.165, G.166, S.167, S.168 Chain C: N.97, G.100, T.101, I.102, D.103, Y.106, E.109, I.110, K.111 Ligands: MG.7 27 PLIP interactions: 6 interactions with chain B, 10 interactions with chain A, 11 interactions with chain C Hydrogen bonds: B:H.165, B:G.166, B:S.167, B:S.168, A:R.84, 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:D.103, C:D.103, C:Y.106, C:K.111, C:K.111 Water bridges: B:S.168, A:L.87, A:R.130, C:T.101, C:A.113, C:A.113 Salt bridges: B:R.160, A:R.84 Hydrophobic interactions: C:Y.106

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

TRS.3: 14 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, L.117 Ligands: TRS.6, TRS.9 11 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: C:S.94, C:I.95, B:S.94, B:I.95, A:S.94, A:I.95 Water bridges: C:S.94, C:S.98, B:S.94, B:I.95, A:I.95 TRS.6: 14 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, L.117 Ligands: TRS.3, TRS.9 11 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: C:S.94, C:I.95, B:S.94, B:I.95, A:S.94, A:I.95 Water bridges: C:S.94, C:S.98, B:I.95, A:S.94, A:S.98 TRS.9: 14 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, L.117 Ligands: TRS.3, TRS.6 11 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: C:S.94, C:I.95, B:S.94, B:I.95, A:S.94, A:I.95 Water bridges: C:S.98, B:S.94, B:S.98, A:S.94, A:I.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Varga, B. et al., Active site of mycobacterial dUTPase: structural characteristics and a built-in sensor. Biochem.Biophys.Res.Commun. (2008)

Release Date

2007-05-22

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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