SMTL ID : 6pc3.1

Crystal structure of Helicobacter pylori PPX/GppA in complex with GSP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x GSP: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE(Non-covalent)

GSP.1: 15 residues within 4Å: Chain A: V.379, Y.380, L.381, A.382, H.383 Chain B: E.44, K.46, R.216, K.220, L.233, G.294, V.295, R.298 Ligands: MG.4, CL.15 21 PLIP interactions: 7 interactions with chain A, 14 interactions with chain B Hydrogen bonds: A:V.379, A:L.381, A:A.382, A:H.383, A:H.383, B:K.46, B:K.46, B:G.294, B:G.294, B:R.298 pi-Stacking: A:Y.380, A:Y.380 Water bridges: B:K.46, B:R.216, B:R.216, B:K.220, B:K.220, B:K.220, B:L.233, B:L.233, B:H.234 GSP.10: 16 residues within 4Å: Chain A: E.44, K.46, R.216, K.220, L.233, G.294, V.295, R.298 Chain B: V.379, Y.380, L.381, A.382, H.383, K.415 Ligands: CL.6, MG.13 21 PLIP interactions: 12 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:K.46, A:K.220, A:G.294, A:G.294, A:R.298, B:V.379, B:L.381, B:A.382, B:H.383, B:H.383 Water bridges: A:R.216, A:R.216, A:R.216, A:L.233, A:L.233, A:L.233, B:Y.380, B:Y.380 Salt bridges: A:E.44 pi-Stacking: B:Y.380, B:Y.380

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

PO4.2: 11 residues within 4Å: Chain A: G.22, S.23, T.94, S.95, E.126, G.149, G.150, G.151, S.152 Ligands: MG.3, K.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.23, A:T.94, A:S.95, A:G.151, A:S.152, A:S.152, A:S.152 Water bridges: A:N.24, A:G.150 PO4.11: 11 residues within 4Å: Chain B: G.22, S.23, T.94, S.95, E.126, G.149, G.150, G.151, S.152 Ligands: MG.12, K.14 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.23, B:T.94, B:S.95, B:G.151, B:S.152, B:S.152 Water bridges: B:N.24, B:G.150

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: E.126 Ligands: PO4.2, K.5, TS6.9 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain A: V.379, Y.380 Ligands: GSP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:V.379, H2O.7, H2O.14 MG.12: 3 residues within 4Å: Chain B: E.126 Ligands: PO4.11, K.14 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain B: V.379 Ligands: GSP.10 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:V.379, H2O.4, H2O.16

2 x K: POTASSIUM ION(Non-covalent)

K.5: 8 residues within 4Å: Chain A: E.126, D.147, I.148, G.149, S.152, E.154 Ligands: PO4.2, MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.147, A:S.152, A:E.154, H2O.1 K.14: 8 residues within 4Å: Chain B: E.126, D.147, I.148, G.149, S.152, E.154 Ligands: PO4.11, MG.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.147, B:S.152, B:E.154, H2O.10

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 5 residues within 4Å: Chain A: R.27, K.46, G.213, R.216 Ligands: GSP.10 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: R.27, R.216, G.296 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain B: R.27, K.46, G.213, R.216 Ligands: GSP.1 Ligand excluded by PLIP

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

EDO.8: 4 residues within 4Å: Chain A: A.13, K.88, D.305, R.308 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.13, A:D.305

2 x TS6: Monothiophosphate(Non-covalent)

TS6.9: 9 residues within 4Å: Chain A: N.24, S.25, R.27, I.148, G.149, G.212, G.213, R.267 Ligands: MG.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.24, A:N.24, A:S.25, A:S.25, A:R.27, A:R.27, A:G.213, A:R.267, A:R.267 Water bridges: A:G.150, A:T.214 TS6.16: 7 residues within 4Å: Chain B: N.24, S.25, R.27, I.148, G.212, G.213, R.267 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.24, B:N.24, B:S.25, B:R.27, B:R.27, B:G.213, B:R.267, B:R.267 Water bridges: B:G.150, B:T.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, H. et al., Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori. Febs J. (2020)

Release Date

2019-11-20

Peptides

Guanosine pentaphosphate phosphohydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Guanosine pentaphosphate phosphohydrolase

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