SMTL ID : 8hrv.1

dutpase of helicobacter pylori 26695

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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: R.133, G.137, F.138, G.139, S.140, T.141 Chain B: V.60, N.76, G.79, T.80, D.82, Y.85, E.88, I.89, K.90 Chain C: R.63, S.64, G.65, Q.111 Ligands: MG.7 23 PLIP interactions: 9 interactions with chain C, 7 interactions with chain A, 7 interactions with chain B Hydrogen bonds: C:R.63, C:S.64, C:S.64, C:S.64, C:G.65, C:Q.111, A:G.137, A:F.138, A:G.139, A:S.140, A:T.141, B:N.76, B:T.80, B:D.82, B:K.90, B:K.90 Water bridges: C:L.66, C:R.108, A:R.133, B:T.80 Salt bridges: C:R.63, A:R.133 Hydrophobic interactions: B:Y.85 DUP.5: 20 residues within 4Å: Chain A: R.63, S.64, G.65, Q.111 Chain B: R.133, G.137, F.138, G.139, S.140, T.141 Chain C: V.60, N.76, G.79, T.80, D.82, Y.85, E.88, I.89, K.90 Ligands: MG.2 27 PLIP interactions: 10 interactions with chain A, 8 interactions with chain C, 9 interactions with chain B Hydrogen bonds: A:R.63, A:R.63, A:S.64, A:S.64, A:S.64, A:G.65, A:Q.111, C:N.76, C:D.82, C:D.82, C:Y.85, C:K.90, C:K.90, B:F.138, B:G.139, B:G.139, B:S.140, B:T.141 Water bridges: A:L.66, A:R.108, C:T.80, B:R.133, B:R.133, B:T.141 Salt bridges: A:R.63, B:R.133 Hydrophobic interactions: C:Y.85 DUP.6: 19 residues within 4Å: Chain A: V.60, N.76, G.79, T.80, D.82, Y.85, E.88, K.90 Chain B: R.63, S.64, G.65, Q.111 Chain C: R.133, G.137, F.138, G.139, S.140, T.141 Ligands: MG.3 25 PLIP interactions: 7 interactions with chain C, 11 interactions with chain B, 7 interactions with chain A Hydrogen bonds: C:G.136, C:F.138, C:G.139, C:S.140, C:T.141, B:R.63, B:R.63, B:S.64, B:S.64, B:S.64, B:G.65, B:Q.111, A:N.76, A:D.82, A:D.82, A:K.90, A:K.90 Water bridges: C:R.133, B:R.63, B:L.66, B:R.108, A:T.80 Salt bridges: C:R.133, B:R.63 Hydrophobic interactions: A:Y.85

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

MG.2: 2 residues within 4Å: Chain B: R.133 Ligands: DUP.5 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain C: R.133 Ligands: DUP.6 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: DUP.1 No protein-ligand interaction detected (PLIP)

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain B: K.3, K.5, S.51, L.52, E.53 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.3, B:K.5, B:S.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumari, K. et al., dutpase of helicobacter pylori 26695. To Be Published

Release Date

2024-01-17

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Deoxyuridine 5'-triphosphate nucleotidohydrolase