SMTL ID : 5ect.1

Mycobacterium tuberculosis dUTPase G143STOP mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-trimer

Ligands

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

DUP.1: 15 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, Q.133 Ligands: MG.3 18 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: A:Y.106 Hydrogen bonds: A:N.97, A:D.103, A:K.111, A:K.111, C:R.84, C:R.84, C:S.85, C:S.85, C:G.86, C:Q.133 Water bridges: A:T.101, B:R.160, B:R.160, C:L.87, C:R.130, C:R.130 Salt bridges: B:R.160 DUP.5: 15 residues within 4Å: Chain A: 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 Ligands: MG.7 18 PLIP interactions: 9 interactions with chain A, 6 interactions with chain B, 3 interactions with chain C Hydrogen bonds: A:R.84, A:R.84, A:S.85, A:S.85, A:G.86, A:Q.133, B:N.97, B:D.103, B:K.111, B:K.111 Water bridges: A:L.87, A:R.130, A:R.130, B:T.101, C:R.160, C:R.160 Hydrophobic interactions: B:Y.106 Salt bridges: C:R.160 DUP.9: 15 residues within 4Å: Chain A: R.160 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.11 18 PLIP interactions: 6 interactions with chain C, 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: C:Y.106 Hydrogen bonds: C:N.97, C:D.103, C:K.111, C:K.111, B:R.84, B:R.84, B:S.85, B:S.85, B:G.86, B:Q.133 Water bridges: C:T.101, B:L.87, B:R.130, B:R.130, A:R.160, A:R.160 Salt bridges: A:R.160

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

TRS.2: 7 residues within 4Å: Chain B: S.94, L.117 Chain C: S.94, I.95, V.96 Ligands: TRS.6, TRS.10 8 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: C:S.94, C:I.95, B:S.94 Water bridges: C:S.94, C:S.98, B:I.95, A:S.94, A:I.95 TRS.6: 7 residues within 4Å: Chain A: S.94, I.95, V.96 Chain C: S.94, L.117 Ligands: TRS.2, TRS.10 8 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A, 2 interactions with chain C Water bridges: B:S.94, B:I.95, A:S.94, A:S.98, C:I.95 Hydrogen bonds: A:S.94, A:I.95, C:S.94 TRS.10: 7 residues within 4Å: Chain A: S.94, L.117 Chain B: S.94, I.95, V.96 Ligands: TRS.2, TRS.6 8 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: B:S.94, B:I.95, A:S.94 Water bridges: B:S.94, B:S.98, A:I.95, C:S.94, C:I.95

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain B: R.160 Ligands: DUP.1 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain C: R.160 Ligands: DUP.5 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain A: R.160 Ligands: DUP.9 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain B: R.84, D.129, R.130 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.84, B:R.84, B:R.130, B:R.130, B:R.130 Water bridges: B:R.90 GOL.8: 3 residues within 4Å: Chain C: R.84, D.129, R.130 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.84, C:R.84, C:R.130, C:R.130, C:R.130 Water bridges: C:R.90 GOL.12: 3 residues within 4Å: Chain A: R.84, D.129, R.130 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.84, A:R.84, A:R.130, A:R.130, A:R.130 Water bridges: A:R.90

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