SMTL ID : 7ooz.1

Purine nucleoside phosphorylase(DeoD-type) from H. pylori with 6-benzyloxo-2-chloropurine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

54 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: T.2, T.74, E.75, K.78, T.79 Chain B: Y.160 Ligands: GOL.10 Ligand excluded by PLIP GOL.2: 7 residues within 4Å: Chain A: P.129, D.130, A.189, N.193, A.194 Chain F: N.174 Ligands: GOL.3 Ligand excluded by PLIP GOL.3: 6 residues within 4Å: Chain A: P.129, D.130, F.131, E.132 Chain F: V.150 Ligands: GOL.2 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: N.6, E.38, I.39, T.40, N.41 Ligand excluded by PLIP GOL.5: 4 residues within 4Å: Chain A: F.32, Q.34, Y.52, K.53 Ligand excluded by PLIP GOL.6: 8 residues within 4Å: Chain A: T.90, C.91, G.92, F.159, I.178, E.179, M.180 Ligands: GOL.8 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain A: D.21, R.24, Y.27 Ligand excluded by PLIP GOL.8: 8 residues within 4Å: Chain A: M.64, R.87, E.179, M.180, E.181 Chain B: R.43 Ligands: GOL.6, MG.9 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: K.78, E.191, L.192 Chain B: Y.160, S.161, F.162 Ligands: GOL.1 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain A: Y.160, S.161, F.162 Chain B: K.78, E.191, L.192 Ligands: GOL.15 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain A: Y.160 Chain B: T.74, E.75, K.78, T.79 Ligands: GOL.14 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain B: P.129, D.130, A.189, M.190, N.193, A.194 Chain C: N.174 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain B: D.204, H.205, K.209, E.210 Ligands: GOL.18 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain B: F.159, Y.160, S.161, T.164, F.167 Ligands: 05Q.11, GOL.17 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain B: N.6, E.38, I.39, T.40, N.41 Ligand excluded by PLIP GOL.20: 2 residues within 4Å: Chain B: D.168, I.207 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain B: L.100, E.210, A.211, L.212, E.216 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain B: S.95, P.96, V.98, G.99, H.205, T.208 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain C: T.2, T.74, E.75, K.78, T.79 Chain D: Y.160 Ligands: GOL.32 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain B: N.174 Chain C: P.129, D.130, A.189, N.193, A.194 Ligands: GOL.25 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain B: V.150 Chain C: P.129, D.130, F.131, E.132 Ligands: GOL.24 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain C: N.6, E.38, I.39, T.40, N.41 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain C: F.32, Q.34, Y.52, K.53 Ligand excluded by PLIP GOL.28: 8 residues within 4Å: Chain C: T.90, C.91, G.92, F.159, I.178, E.179, M.180 Ligands: GOL.30 Ligand excluded by PLIP GOL.29: 3 residues within 4Å: Chain C: D.21, R.24, Y.27 Ligand excluded by PLIP GOL.30: 8 residues within 4Å: Chain C: M.64, R.87, E.179, M.180, E.181 Chain D: R.43 Ligands: GOL.28, MG.31 Ligand excluded by PLIP GOL.32: 7 residues within 4Å: Chain C: K.78, E.191, L.192 Chain D: Y.160, S.161, F.162 Ligands: GOL.23 Ligand excluded by PLIP GOL.36: 7 residues within 4Å: Chain C: Y.160, S.161, F.162 Chain D: K.78, E.191, L.192 Ligands: GOL.37 Ligand excluded by PLIP GOL.37: 6 residues within 4Å: Chain C: Y.160 Chain D: T.74, E.75, K.78, T.79 Ligands: GOL.36 Ligand excluded by PLIP GOL.38: 7 residues within 4Å: Chain D: P.129, D.130, A.189, M.190, N.193, A.194 Chain E: N.174 Ligand excluded by PLIP GOL.39: 5 residues within 4Å: Chain D: D.204, H.205, K.209, E.210 Ligands: GOL.40 Ligand excluded by PLIP GOL.40: 7 residues within 4Å: Chain D: F.159, Y.160, S.161, T.164, F.167 Ligands: 05Q.33, GOL.39 Ligand excluded by PLIP GOL.41: 5 residues within 4Å: Chain D: N.6, E.38, I.39, T.40, N.41 Ligand excluded by PLIP GOL.42: 2 residues within 4Å: Chain D: D.168, I.207 Ligand excluded by PLIP GOL.43: 5 residues within 4Å: Chain D: L.100, E.210, A.211, L.212, E.216 Ligand excluded by PLIP GOL.44: 6 residues within 4Å: Chain D: S.95, P.96, V.98, G.99, H.205, T.208 Ligand excluded by PLIP GOL.45: 7 residues within 4Å: Chain E: T.2, T.74, E.75, K.78, T.79 Chain F: Y.160 Ligands: GOL.54 Ligand excluded by PLIP GOL.46: 7 residues within 4Å: Chain D: N.174 Chain E: P.129, D.130, A.189, N.193, A.194 Ligands: GOL.47 Ligand excluded by PLIP GOL.47: 6 residues within 4Å: Chain D: V.150 Chain E: P.129, D.130, F.131, E.132 Ligands: GOL.46 Ligand excluded by PLIP GOL.48: 5 residues within 4Å: Chain E: N.6, E.38, I.39, T.40, N.41 Ligand excluded by PLIP GOL.49: 4 residues within 4Å: Chain E: F.32, Q.34, Y.52, K.53 Ligand excluded by PLIP GOL.50: 8 residues within 4Å: Chain E: T.90, C.91, G.92, F.159, I.178, E.179, M.180 Ligands: GOL.52 Ligand excluded by PLIP GOL.51: 3 residues within 4Å: Chain E: D.21, R.24, Y.27 Ligand excluded by PLIP GOL.52: 8 residues within 4Å: Chain E: M.64, R.87, E.179, M.180, E.181 Chain F: R.43 Ligands: GOL.50, MG.53 Ligand excluded by PLIP GOL.54: 7 residues within 4Å: Chain E: K.78, E.191, L.192 Chain F: Y.160, S.161, F.162 Ligands: GOL.45 Ligand excluded by PLIP GOL.58: 7 residues within 4Å: Chain E: Y.160, S.161, F.162 Chain F: K.78, E.191, L.192 Ligands: GOL.59 Ligand excluded by PLIP GOL.59: 6 residues within 4Å: Chain E: Y.160 Chain F: T.74, E.75, K.78, T.79 Ligands: GOL.58 Ligand excluded by PLIP GOL.60: 7 residues within 4Å: Chain A: N.174 Chain F: P.129, D.130, A.189, M.190, N.193, A.194 Ligand excluded by PLIP GOL.61: 5 residues within 4Å: Chain F: D.204, H.205, K.209, E.210 Ligands: GOL.62 Ligand excluded by PLIP GOL.62: 7 residues within 4Å: Chain F: F.159, Y.160, S.161, T.164, F.167 Ligands: 05Q.55, GOL.61 Ligand excluded by PLIP GOL.63: 5 residues within 4Å: Chain F: N.6, E.38, I.39, T.40, N.41 Ligand excluded by PLIP GOL.64: 2 residues within 4Å: Chain F: D.168, I.207 Ligand excluded by PLIP GOL.65: 5 residues within 4Å: Chain F: L.100, E.210, A.211, L.212, E.216 Ligand excluded by PLIP GOL.66: 6 residues within 4Å: Chain F: S.95, P.96, V.98, G.99, H.205, T.208 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 4 residues within 4Å: Chain A: G.89, T.90 Chain B: R.43 Ligands: GOL.8 No protein-ligand interaction detected (PLIP) MG.31: 4 residues within 4Å: Chain C: G.89, T.90 Chain D: R.43 Ligands: GOL.30 No protein-ligand interaction detected (PLIP) MG.53: 4 residues within 4Å: Chain E: G.89, T.90 Chain F: R.43 Ligands: GOL.52 No protein-ligand interaction detected (PLIP)

3 x 05Q: 6-benzyloxo-2-chloropurine(Non-covalent)

05Q.11: 16 residues within 4Å: Chain B: T.90, C.91, G.92, A.93, I.94, F.158, F.159, F.167, I.178, E.179, M.180, S.203, D.204, L.206 Ligands: TRS.12, GOL.18 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.94, B:F.167, B:I.178, B:L.206 Hydrogen bonds: B:T.90, B:D.204 pi-Stacking: B:F.159 Halogen bonds: B:F.158 05Q.33: 16 residues within 4Å: Chain D: T.90, C.91, G.92, A.93, I.94, F.158, F.159, F.167, I.178, E.179, M.180, S.203, D.204, L.206 Ligands: TRS.34, GOL.40 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.94, D:F.167, D:I.178, D:L.206 Hydrogen bonds: D:D.204 pi-Stacking: D:F.159 Halogen bonds: D:F.158 05Q.55: 16 residues within 4Å: Chain F: T.90, C.91, G.92, A.93, I.94, F.158, F.159, F.167, I.178, E.179, M.180, S.203, D.204, L.206 Ligands: TRS.56, GOL.62 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:I.94, F:F.167, F:I.178, F:L.206 Hydrogen bonds: F:T.90, F:D.204 pi-Stacking: F:F.159 Halogen bonds: F:F.158

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

TRS.12: 11 residues within 4Å: Chain A: H.4, R.43 Chain B: M.64, R.87, T.90, F.159, E.179, M.180, E.181 Ligands: 05Q.11, PO4.13 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:H.4, B:R.87, B:T.90, B:T.90, B:M.180 Water bridges: A:R.43, B:S.203 TRS.34: 11 residues within 4Å: Chain C: H.4, R.43 Chain D: M.64, R.87, T.90, F.159, E.179, M.180, E.181 Ligands: 05Q.33, PO4.35 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:H.4, D:R.87, D:T.90, D:M.180 Water bridges: C:R.43, D:S.203 TRS.56: 11 residues within 4Å: Chain E: H.4, R.43 Chain F: M.64, R.87, T.90, F.159, E.179, M.180, E.181 Ligands: 05Q.55, PO4.57 7 PLIP interactions: 5 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:R.87, F:T.90, F:T.90, F:M.180, E:H.4 Water bridges: F:S.203, E:R.43

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

PO4.13: 10 residues within 4Å: Chain A: R.43 Chain B: C.19, G.20, D.21, R.24, R.87, G.89, T.90, E.181 Ligands: TRS.12 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.20, B:D.21, B:T.90, B:T.90, B:T.90 Water bridges: B:S.203 Salt bridges: B:R.24, B:R.87, A:R.43 PO4.35: 10 residues within 4Å: Chain C: R.43 Chain D: C.19, G.20, D.21, R.24, R.87, G.89, T.90, E.181 Ligands: TRS.34 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.20, D:D.21, D:T.90, D:T.90, D:T.90 Water bridges: D:S.203 Salt bridges: D:R.24, D:R.87, C:R.43 PO4.57: 10 residues within 4Å: Chain E: R.43 Chain F: C.19, G.20, D.21, R.24, R.87, G.89, T.90, E.181 Ligands: TRS.56 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.20, F:D.21, F:T.90, F:T.90, F:T.90 Water bridges: F:S.203 Salt bridges: F:R.24, F:R.87, E:R.43

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
A

B
B

C
A

D
B

E
A

F
B

Purine nucleoside phosphorylase DeoD-type

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