SMTL ID : 4gcy.1

Structure of Mycobacterium tuberculosis dUTPase H21W mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

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

DUP.1: 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.3 25 PLIP interactions: 10 interactions with chain B, 9 interactions with chain A, 6 interactions with chain C Hydrogen bonds: B:R.84, B:R.84, B:S.85, B:S.85, B:S.85, B:G.86, B:Q.133, A:N.97, A:T.101, A:D.103, A:D.103, A:Y.106, A:K.111, A:K.111, C:H.165, C:G.166, C:S.167, C:S.168 Water bridges: B:L.87, B:R.130, A:T.101, C:S.168 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.7 25 PLIP interactions: 10 interactions with chain C, 6 interactions with chain A, 9 interactions with chain B Hydrogen bonds: C:R.84, C:R.84, C:S.85, C:S.85, C:S.85, C:G.86, C:Q.133, A:H.165, A:G.166, A:S.167, A:S.168, B:N.97, B:T.101, B:D.103, B:D.103, B:Y.106, B:K.111, B:K.111 Water bridges: C:L.87, C:R.130, A:S.168, B:T.101 Salt bridges: C:R.84, A:R.160 Hydrophobic interactions: B:Y.106 DUP.9: 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.11 25 PLIP interactions: 10 interactions with chain A, 9 interactions with chain C, 6 interactions with chain B Hydrogen bonds: 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, B:H.165, B:G.166, B:S.167, B:S.168 Water bridges: A:L.87, A:R.130, C:T.101, B:S.168 Salt bridges: A:R.84, B:R.160 Hydrophobic interactions: C:Y.106

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

TRS.2: 7 residues within 4Å: Chain A: S.94, I.95, V.96 Chain B: S.94, L.117 Ligands: TRS.6, TRS.10 7 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 5 interactions with chain A Hydrogen bonds: B:S.94, A:S.94, A:I.95 Water bridges: C:I.95, A:S.94, A:I.95, A:V.96 TRS.6: 7 residues within 4Å: Chain B: S.94, I.95, V.96 Chain C: S.94, L.117 Ligands: TRS.2, TRS.10 7 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:S.94, B:I.95, C:S.94 Water bridges: B:S.94, B:I.95, B:V.96, A:I.95 TRS.10: 7 residues within 4Å: Chain A: S.94, L.117 Chain C: S.94, I.95, V.96 Ligands: TRS.2, TRS.6 7 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:S.94, C:S.94, C:I.95 Water bridges: A:S.98, C:S.94, C:S.98, B:I.95

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain C: R.160 Ligands: DUP.1 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain A: R.160 Ligands: DUP.5 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: 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 A: G.170 Chain C: Y.50, R.130 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Water bridges: A:G.170 Hydrogen bonds: C:R.130, C:R.130 GOL.8: 3 residues within 4Å: Chain A: Y.50, R.130 Chain B: G.170 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.130, A:R.130 Water bridges: B:G.170 GOL.12: 3 residues within 4Å: Chain B: Y.50, R.130 Chain C: G.170 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.130, B:R.130 Water bridges: C:G.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Toth, J. et al., RAMD identification of substrate binding pathways to the active site of dUTPase. To be Published

Release Date

2013-07-03

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Deoxyuridine 5'-triphosphate nucleotidohydrolase