SMTL ID : 5lu0.1

Crystal structure of H. pylori referent strain in complex with PO4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 10 residues within 4Å: Chain A: C.19, G.20, D.21, R.24, R.87, G.89, T.90, E.181 Chain D: R.43 Ligands: TRS.2 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 Salt bridges: A:R.24, A:R.87, D:R.43 PO4.4: 10 residues within 4Å: Chain B: C.19, G.20, D.21, R.24, R.87, G.89, T.90, E.181 Chain E: R.43 Ligands: TRS.5 8 PLIP interactions: 7 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:S.203 Salt bridges: B:R.24, B:R.87, E:R.43 PO4.11: 10 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 Ligands: TRS.12 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:G.20, C:D.21, C:T.90, C:T.90 Water bridges: C:S.203 Salt bridges: C:R.24, C:R.87, F:R.43 PO4.15: 10 residues within 4Å: Chain B: R.43 Chain E: C.19, G.20, D.21, R.24, R.87, G.89, T.90, E.181 Ligands: TRS.16 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:G.20, E:D.21, E:T.90, E:T.90, E:T.90 Salt bridges: E:R.24, E:R.87, B:R.43

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

TRS.2: 10 residues within 4Å: Chain A: M.64, R.87, T.90, F.159, E.179, M.180, E.181 Chain D: H.4, R.43 Ligands: PO4.1 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.87, A:M.180, D:H.4, D:R.43 Water bridges: A:T.90, A:T.90, A:R.217 TRS.5: 10 residues within 4Å: Chain B: M.64, R.87, T.90, F.159, E.179, M.180, E.181 Chain E: H.4, R.43 Ligands: PO4.4 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain E Hydrogen bonds: B:R.87, B:T.90, B:M.180, E:H.4, E:R.43, E:R.43 Water bridges: B:S.203, B:D.204, B:R.217 TRS.12: 10 residues within 4Å: Chain C: M.64, R.87, T.90, F.159, E.179, M.180, E.181 Chain F: H.4, R.43 Ligands: PO4.11 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:R.87, C:T.90, C:T.90, C:M.180, F:R.43, F:R.43 Water bridges: C:S.203, C:D.204 TRS.16: 10 residues within 4Å: Chain B: R.43 Chain E: M.64, R.87, T.90, C.91, I.178, E.179, M.180, E.181 Ligands: PO4.15 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:R.87, E:T.90, E:T.90, E:I.178, E:M.180, B:R.43, B:R.43 Water bridges: E:T.90, E:G.92

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

EDO.3: 5 residues within 4Å: Chain A: T.74, K.78, E.191 Chain D: Y.160, F.162 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:K.78 Water bridges: A:T.74, A:R.119, A:E.191, D:S.161, D:S.161 EDO.6: 3 residues within 4Å: Chain B: E.75, K.78, T.79 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.79 EDO.7: 5 residues within 4Å: Chain B: T.74, K.78, E.191 Chain E: Y.160, F.162 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:E.191 Water bridges: B:R.119, E:S.161 EDO.8: 5 residues within 4Å: Chain B: L.23, P.214, V.218 Chain E: N.6, V.42 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.6 Water bridges: E:R.43 EDO.9: 5 residues within 4Å: Chain B: N.6, E.38, I.39, T.40, N.41 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.38, B:E.38 Water bridges: B:I.39, B:N.41 EDO.10: 3 residues within 4Å: Chain B: Y.27, K.30, E.219 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.30, B:E.219, B:E.219 EDO.13: 1 residues within 4Å: Chain C: T.208 No protein-ligand interaction detected (PLIP) EDO.14: 4 residues within 4Å: Chain A: Y.160, F.162 Chain D: K.78, E.191 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:E.191 Water bridges: D:K.78, D:K.78, D:R.119, A:Y.160, A:S.161 EDO.17: 6 residues within 4Å: Chain B: Y.160, F.162 Chain E: T.74, K.78, E.191, L.192 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain E Water bridges: B:Y.160, B:S.161, E:K.78, E:R.119 EDO.18: 6 residues within 4Å: Chain C: Y.160, F.162 Chain F: T.74, K.78, E.191, L.192 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain F Water bridges: C:Y.160, C:S.161, F:T.74, F:K.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Narczyk, M. et al., Helicobacter pylori purine nucleoside phosphorylase shows new distribution patterns of open and closed active site conformations and unusual biochemical features. FEBS J. (2018)

Release Date

2017-09-20

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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