SMTL ID : 5edd.1

Crystal structure of Mycobacterium tuberculosis dUTPase R140K, H145W mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-trimer

Ligands

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

TRS.1: 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.4, TRS.7 11 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A, 4 interactions with chain C Hydrogen bonds: B:S.94, B:I.95, A:S.94, A:I.95, C:S.94, C:I.95 Water bridges: B:I.95, A:S.94, A:S.98, C:S.94, C:S.98 TRS.4: 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.1, TRS.7 11 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A, 3 interactions with chain C Hydrogen bonds: B:S.94, B:I.95, A:S.94, A:I.95, C:S.94, C:I.95 Water bridges: B:S.94, B:S.98, A:S.94, A:I.95, C:S.98 TRS.7: 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.1, TRS.4 11 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A, 4 interactions with chain C Hydrogen bonds: B:S.94, B:I.95, A:S.94, A:I.95, C:S.94, C:I.95 Water bridges: B:S.94, B:I.95, A:I.95, C:S.94, C:S.98

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

DUP.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.84, S.85, G.86, Q.133 Ligands: MG.3 22 PLIP interactions: 13 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:R.84, B:S.85, B:S.85, B:G.86, B:Q.133, A:N.97, A:D.103, A:D.103, A:Y.106, A:K.111, A:K.111 Water bridges: B:D.44, B:R.84, B:R.84, B:R.90, B:R.130, B:R.130, B:Q.133, A:T.101 Salt bridges: B:R.84 Hydrophobic interactions: A:I.102, A:Y.106 DUP.5: 14 residues within 4Å: 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.6 22 PLIP interactions: 13 interactions with chain C, 9 interactions with chain B Hydrogen bonds: C:R.84, C:S.85, C:S.85, C:G.86, C:Q.133, B:N.97, B:D.103, B:D.103, B:Y.106, B:K.111, B:K.111 Water bridges: C:D.44, C:R.84, C:R.84, C:R.90, C:R.130, C:R.130, C:Q.133, B:T.101 Salt bridges: C:R.84 Hydrophobic interactions: B:I.102, B:Y.106 DUP.8: 14 residues within 4Å: Chain A: 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.9 22 PLIP interactions: 13 interactions with chain A, 9 interactions with chain C Hydrogen bonds: A:R.84, A:S.85, A:S.85, A:G.86, A:Q.133, C:N.97, C:D.103, C:D.103, C:Y.106, C:K.111, C:K.111 Water bridges: A:D.44, A:R.84, A:R.84, A:R.90, A:R.130, A:R.130, A:Q.133, C:T.101 Salt bridges: A:R.84 Hydrophobic interactions: C:I.102, C:Y.106

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain B: D.48 Ligands: DUP.2 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain C: D.48 Ligands: DUP.5 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain A: D.48 Ligands: DUP.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagy, G.N. et al., Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases. J. Am. Chem. Soc. (2016)

Release Date

2016-11-02

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Deoxyuridine 5'-triphosphate nucleotidohydrolase