SMTL ID : 7op9.2 (1 other biounit)

Purine nucleoside phosphorylase(DeoD-type) from H. pylori with 2,6-dichloropurine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-hexamer

Ligands

6 x 06K: 2,6-bis(chloranyl)-7H-purine(Non-covalent)

06K.1: 11 residues within 4Å: Chain A: T.90, C.91, G.92, F.158, F.159, I.178, E.179, M.180, D.204, L.206 Ligands: IMD.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.179 Water bridges: A:T.90 Halogen bonds: A:D.204 06K.4: 11 residues within 4Å: Chain B: T.90, C.91, G.92, F.158, F.159, I.178, E.179, M.180, D.204, L.206 Ligands: IMD.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.179 Water bridges: B:T.90 pi-Stacking: B:F.159, B:F.159 Halogen bonds: B:D.204 06K.7: 11 residues within 4Å: Chain C: T.90, C.91, G.92, F.158, F.159, I.178, E.179, M.180, D.204, L.206 Ligands: IMD.17 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.179 Water bridges: C:T.90 Halogen bonds: C:D.204 06K.10: 11 residues within 4Å: Chain D: T.90, C.91, G.92, F.158, F.159, I.178, E.179, M.180, D.204, L.206 Ligands: IMD.2 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.179 Halogen bonds: D:D.204 06K.13: 11 residues within 4Å: Chain E: T.90, C.91, G.92, F.158, F.159, I.178, E.179, M.180, D.204, L.206 Ligands: IMD.5 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.179 Water bridges: E:D.204 Halogen bonds: E:D.204 06K.16: 11 residues within 4Å: Chain F: T.90, C.91, G.92, F.158, F.159, I.178, E.179, M.180, D.204, L.206 Ligands: IMD.8 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.179 Water bridges: F:D.204 Halogen bonds: F:D.204

6 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 7 residues within 4Å: Chain A: H.4, R.43 Chain D: M.64, F.159, M.180 Ligands: 06K.10, MG.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.43 pi-Cation interactions: A:R.43 IMD.5: 7 residues within 4Å: Chain B: H.4, R.43 Chain E: M.64, F.159, M.180 Ligands: 06K.13, MG.15 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:T.90, B:R.43 pi-Cation interactions: B:R.43 IMD.8: 7 residues within 4Å: Chain C: H.4, R.43 Chain F: M.64, F.159, M.180 Ligands: 06K.16, MG.18 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:R.43, F:T.90 pi-Cation interactions: C:R.43 Water bridges: F:T.90 IMD.11: 8 residues within 4Å: Chain A: M.64, T.90, F.159, M.180 Chain D: H.4, R.43 Ligands: 06K.1, MG.3 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:T.90, A:T.90, D:R.43 Water bridges: A:T.90, D:R.43 pi-Cation interactions: D:R.43 IMD.14: 7 residues within 4Å: Chain B: M.64, F.159, M.180 Chain E: H.4, R.43 Ligands: 06K.4, MG.6 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain E Hydrogen bonds: B:T.90, B:T.90, E:R.43 Water bridges: B:T.90, E:R.43 pi-Cation interactions: E:R.43 IMD.17: 8 residues within 4Å: Chain C: M.64, T.90, F.159, M.180 Chain F: H.4, R.43 Ligands: 06K.7, MG.9 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain C Hydrogen bonds: F:R.43, C:T.90, C:T.90 Water bridges: F:R.43, C:T.90 pi-Cation interactions: F:R.43

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: R.24, G.89, T.90 Chain D: R.43 Ligands: IMD.11 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain B: R.24, G.89, T.90 Chain E: R.43 Ligands: IMD.14 No protein-ligand interaction detected (PLIP) MG.9: 5 residues within 4Å: Chain C: R.24, G.89, T.90 Chain F: R.43 Ligands: IMD.17 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain A: R.43 Chain D: R.24, G.89, T.90 Ligands: IMD.2 No protein-ligand interaction detected (PLIP) MG.15: 5 residues within 4Å: Chain B: R.43 Chain E: R.24, G.89, T.90 Ligands: IMD.5 No protein-ligand interaction detected (PLIP) MG.18: 5 residues within 4Å: Chain C: R.43 Chain F: R.24, G.89, T.90 Ligands: IMD.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Narczyk, M. et al., Interactions of 2,6-substituted purines with purine nucleoside phosphorylase from Helicobacter pylori in solution and in the crystal, and the effects of these compounds on cell cultures of this bacterium. J Enzyme Inhib Med Chem (2022)

Release Date

2022-05-04

Peptides

Purine nucleoside phosphorylase DeoD-type: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

Purine nucleoside phosphorylase DeoD-type

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