SMTL ID : 5mx6.1

Crystal structure of H. pylori purine nucleoside phosphorylase from clinical isolate HpPNP-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-hexamer

Ligands

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 7 residues within 4Å: Chain A: C.19, G.20, D.21, R.87, G.89, T.90 Chain D: R.43 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.20, A:D.21, A:T.90, A:T.90 Water bridges: A:R.87 Salt bridges: A:R.87, D:R.43 SO4.3: 3 residues within 4Å: Chain A: Q.34, D.35, A.36 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.35, A:A.36 Water bridges: A:L.33 SO4.6: 8 residues within 4Å: Chain B: C.19, G.20, D.21, R.24, R.87, G.89, T.90 Chain E: R.43 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:G.20, B:D.21, B:T.90, B:T.90 Water bridges: B:R.87 Salt bridges: B:R.87, E:R.43 SO4.11: 3 residues within 4Å: Chain C: L.33, Q.34, D.35 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.35 Water bridges: C:A.36, C:A.36 SO4.13: 9 residues within 4Å: Chain A: R.43 Chain D: C.19, G.20, D.21, R.24, R.87, G.89, T.90, E.181 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain D Water bridges: A:R.43, D:R.87, D:R.87 Salt bridges: A:R.43, D:R.24, D:R.87 Hydrogen bonds: D:G.20, D:D.21, D:T.90 SO4.15: 4 residues within 4Å: Chain D: L.33, Q.34, D.35, A.36 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.33, D:D.35, D:A.36 SO4.17: 8 residues within 4Å: Chain B: R.43 Chain E: C.19, G.20, D.21, R.24, R.87, G.89, T.90 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:G.20, E:D.21, E:R.24, E:T.90, E:T.90 Salt bridges: E:R.87, B:R.43 SO4.20: 7 residues within 4Å: Chain C: R.43 Chain F: G.20, D.21, R.24, R.87, G.89, T.90 10 PLIP interactions: 8 interactions with chain F, 2 interactions with chain C Hydrogen bonds: F:G.20, F:D.21, F:T.90, F:T.90 Water bridges: F:G.63, F:R.87, C:R.43 Salt bridges: F:R.24, F:R.87, C:R.43 SO4.22: 2 residues within 4Å: Chain F: Q.34, D.35 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.35, F:D.35 Water bridges: F:Q.34

6 x HPA: HYPOXANTHINE(Non-covalent)

HPA.2: 9 residues within 4Å: Chain A: T.90, C.91, G.92, F.159, I.178, E.179, M.180, D.204, L.206 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.90, A:D.204 Water bridges: A:F.159, A:M.180 HPA.7: 8 residues within 4Å: Chain B: T.90, C.91, G.92, F.159, I.178, M.180, D.204, L.206 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.204 HPA.10: 10 residues within 4Å: Chain C: T.90, C.91, G.92, F.159, I.178, E.179, M.180, S.203, D.204, L.206 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.90, C:F.159, C:D.204 HPA.14: 9 residues within 4Å: Chain D: T.90, C.91, G.92, F.159, I.178, E.179, M.180, D.204, L.206 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.90, D:D.204 Water bridges: D:M.180 HPA.18: 7 residues within 4Å: Chain E: T.90, C.91, G.92, F.159, I.178, E.179, L.206 1 PLIP interactions: 1 interactions with chain E Water bridges: E:M.180 HPA.21: 6 residues within 4Å: Chain F: T.90, C.91, G.92, F.159, I.178, L.206 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:T.90, F:S.203 Water bridges: F:F.159

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 5 residues within 4Å: Chain A: K.78, E.191 Chain D: Y.160, S.161, F.162 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Salt bridges: A:K.78 Hydrophobic interactions: D:Y.160 ACT.23: 5 residues within 4Å: Chain C: Y.160, S.161, F.162 Chain F: K.78, E.191 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain C Water bridges: F:T.74, F:K.78, F:R.119 Salt bridges: F:K.78 Hydrophobic interactions: C:Y.160, C:F.162

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 6 residues within 4Å: Chain A: N.122 Chain B: N.122 Chain C: N.122 Chain D: N.122 Chain E: N.122 Chain F: N.122 11 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, 1 interactions with chain C, 1 interactions with chain F, 2 interactions with chain D, 2 interactions with chain E Hydrogen bonds: A:N.122, B:N.122, C:N.122, F:N.122, E:N.122, E:N.122 Water bridges: A:R.117, A:R.117, B:R.117, D:R.117, D:R.117 PEG.8: 3 residues within 4Å: Chain B: N.6, E.38, N.41 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.6 PEG.12: 4 residues within 4Å: Chain C: N.6, E.38, I.39, N.41 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.38 PEG.16: 4 residues within 4Å: Chain D: N.6, E.38, I.39, N.41 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.6, D:E.38 PEG.19: 4 residues within 4Å: Chain E: N.6, E.38, I.39, N.41 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.41

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.9: 9 residues within 4Å: Chain C: C.19, G.20, D.21, R.24, R.87, G.89, T.90, E.181 Chain F: R.43 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:G.20, C:D.21, C:T.90 Water bridges: C:R.87 Salt bridges: C:R.24, C:R.87, F:R.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stefanic, Z. et al., Structural characterization of purine nucleoside phosphorylase from human pathogen Helicobacter pylori. Int. J. Biol. Macromol. (2017)

Release Date

2017-04-05

Peptides

Purine nucleoside phosphorylase DeoD-type: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Purine nucleoside phosphorylase DeoD-type

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