SMTL ID : 6g7x.1

Crystal structure of H. pylori purine nucleoside phosphorylase soaked in PO4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-hexamer

Ligands

23 x IMD: IMIDAZOLE(Non-covalent)

IMD.1: 6 residues within 4Å: Chain A: H.4, R.43 Chain D: M.64, F.159, M.180 Ligands: PO4.19 Ligand excluded by PLIP IMD.2: 3 residues within 4Å: Chain A: G.92, F.159, I.178 Ligand excluded by PLIP IMD.3: 5 residues within 4Å: Chain A: N.6, E.38, I.39, T.40, N.41 Ligand excluded by PLIP IMD.5: 6 residues within 4Å: Chain B: H.4, R.43 Chain E: M.64, F.159, M.180 Ligands: PO4.24 Ligand excluded by PLIP IMD.6: 2 residues within 4Å: Chain B: F.159, I.178 Ligand excluded by PLIP IMD.7: 5 residues within 4Å: Chain B: N.6, E.38, I.39, T.40, N.41 Ligand excluded by PLIP IMD.8: 8 residues within 4Å: Chain A: K.114, R.117, V.118, N.122 Chain B: L.121, N.122, H.123 Chain D: E.163 Ligand excluded by PLIP IMD.9: 6 residues within 4Å: Chain B: K.114, R.117, V.118, N.122 Chain C: L.121, H.123 Ligand excluded by PLIP IMD.11: 6 residues within 4Å: Chain C: H.4, R.43 Chain F: M.64, F.159, M.180 Ligands: PO4.29 Ligand excluded by PLIP IMD.12: 3 residues within 4Å: Chain C: F.159, I.178, M.180 Ligand excluded by PLIP IMD.13: 5 residues within 4Å: Chain C: N.6, E.38, I.39, T.40, N.41 Ligand excluded by PLIP IMD.14: 7 residues within 4Å: Chain A: L.121, N.122, H.123 Chain C: K.114, V.118, N.122 Chain F: E.163 Ligand excluded by PLIP IMD.16: 4 residues within 4Å: Chain D: F.158, F.159, I.178, M.180 Ligand excluded by PLIP IMD.17: 7 residues within 4Å: Chain A: M.64, T.90, F.159, M.180 Chain D: H.4, R.43 Ligands: PO4.4 Ligand excluded by PLIP IMD.18: 2 residues within 4Å: Chain D: N.6, N.41 Ligand excluded by PLIP IMD.20: 3 residues within 4Å: Chain E: G.92, F.159, I.178 Ligand excluded by PLIP IMD.21: 7 residues within 4Å: Chain B: M.64, T.90, F.159, M.180 Chain E: H.4, R.43 Ligands: PO4.10 Ligand excluded by PLIP IMD.22: 4 residues within 4Å: Chain E: N.6, E.38, I.39, N.41 Ligand excluded by PLIP IMD.23: 8 residues within 4Å: Chain B: E.163 Chain D: L.121, N.122, H.123 Chain E: K.114, R.117, V.118, N.122 Ligand excluded by PLIP IMD.25: 3 residues within 4Å: Chain F: F.159, I.178, L.206 Ligand excluded by PLIP IMD.26: 6 residues within 4Å: Chain C: M.64, F.159, M.180 Chain F: H.4, R.43 Ligands: PO4.15 Ligand excluded by PLIP IMD.27: 4 residues within 4Å: Chain F: N.6, E.38, I.39, N.41 Ligand excluded by PLIP IMD.28: 7 residues within 4Å: Chain E: L.121, N.122, H.123 Chain F: K.114, R.117, V.118, N.122 Ligand excluded by PLIP

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

PO4.4: 8 residues within 4Å: Chain A: C.19, G.20, D.21, R.24, G.89, T.90 Chain D: R.43 Ligands: IMD.17 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:G.20, A:D.21, A:T.90 Water bridges: A:R.87, A:R.87, A:R.87, A:R.87, A:R.87, D:R.43, D:R.43 Salt bridges: A:R.24, D:R.43 PO4.10: 10 residues within 4Å: Chain B: C.19, G.20, D.21, R.24, R.87, G.89, T.90, F.221 Chain E: R.43 Ligands: IMD.21 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain E Hydrogen bonds: B:G.20, B:D.21, B:R.87, B:T.90, B:T.90, B:T.90 Water bridges: B:R.87, B:I.88, B:E.179, E:R.43, E:R.43 Salt bridges: B:R.24, E:R.43 PO4.15: 9 residues within 4Å: Chain C: C.19, G.20, D.21, R.24, R.87, G.89, T.90 Chain F: R.43 Ligands: IMD.26 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain F Hydrogen bonds: C:G.20, C:D.21, C:R.87, C:T.90, C:T.90 Water bridges: C:R.87, C:R.87, F:R.43, F:R.43 Salt bridges: C:R.24, F:R.43 PO4.19: 7 residues within 4Å: Chain A: R.43 Chain D: C.19, D.21, R.24, G.89, T.90 Ligands: IMD.1 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:D.21, D:T.90 Water bridges: D:G.20, D:R.24, D:R.87, D:R.87, A:R.43, A:R.43, A:R.43 Salt bridges: D:R.24, A:R.43 PO4.24: 8 residues within 4Å: Chain B: R.43 Chain E: C.19, G.20, D.21, R.24, G.89, T.90 Ligands: IMD.5 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:G.20, E:D.21, E:T.90, E:T.90 Water bridges: E:R.87, E:R.87, E:R.87 Salt bridges: E:R.24, B:R.43 PO4.29: 7 residues within 4Å: Chain C: R.43 Chain F: C.19, G.20, R.24, G.89, T.90 Ligands: IMD.11 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:G.20, F:R.24, F:T.90, F:T.90 Water bridges: F:R.24, F:R.87, F:R.87 Salt bridges: C:R.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bosnjakovic, M. et al., The Role of Phosphate Binding in Purine Nucleoside Phosphorylase of Helicobacter pylori. Croatica Chemica Acta (2018)

Release Date

2018-08-08

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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