SMTL ID : 6pc1.1 (1 other biounit)

Crystal structure of Helicobacter pylori PPX/GppA (E143A) in complex with ppGpp

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.76 Å

Oligo State

homo-dimer

Ligands

2 x G4P: GUANOSINE-5',3'-TETRAPHOSPHATE(Non-covalent)

G4P.1: 11 residues within 4Å: Chain A: R.27, K.46, R.216, K.220, L.233, N.264, R.267, G.294 Chain B: Y.380, L.381, K.415 27 PLIP interactions: 19 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:K.220, A:K.220, A:N.264, A:G.294, A:G.294, B:Y.380, B:L.381 Water bridges: A:L.233, A:L.233, A:L.233, A:H.234, A:R.267, A:R.267, A:R.267, B:A.382, B:K.415, B:K.415 Salt bridges: A:R.27, A:E.44, A:K.46, A:K.46, A:R.216, A:K.220, A:R.267, B:K.415 pi-Stacking: B:Y.380, B:Y.380 G4P.7: 12 residues within 4Å: Chain A: Y.380, L.381, K.415 Chain B: R.27, K.46, R.216, K.220, L.233, N.264, E.266, R.267, G.294 23 PLIP interactions: 5 interactions with chain A, 18 interactions with chain B Hydrogen bonds: A:L.381, B:K.220, B:K.220, B:H.234, B:N.264, B:G.294, B:G.294 Water bridges: A:S.413, B:R.216, B:L.233, B:L.233, B:R.298 Salt bridges: A:K.415, B:R.27, B:E.44, B:K.46, B:K.46, B:R.216, B:K.220, B:K.220, B:R.267 pi-Stacking: A:Y.380, A:Y.380

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

PO4.2: 8 residues within 4Å: Chain A: S.23, T.94, S.95, E.126, G.149, G.150, G.151, S.152 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.23, A:S.23, A:T.94, A:T.94, A:S.95, A:G.150, A:G.151, A:S.152, A:S.152 Water bridges: A:G.149, A:G.149 PO4.8: 9 residues within 4Å: Chain B: S.23, T.94, S.95, E.126, G.149, G.150, G.151, S.152 Ligands: MG.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.23, B:T.94, B:S.95, B:E.126, B:E.126, B:G.150, B:G.151, B:S.152 Water bridges: B:N.24

3 x LMR: (2S)-2-hydroxybutanedioic acid(Non-covalent)

LMR.3: 8 residues within 4Å: Chain A: N.24, S.25, R.27, G.212, G.213, R.216, R.267, R.298 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.24, A:G.213 Water bridges: A:T.214, A:T.214, A:V.297, A:R.298, A:R.298 Salt bridges: A:R.27, A:R.216, A:R.267, A:R.298 LMR.4: 1 residues within 4Å: Chain A: K.478 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Salt bridges: B:K.72, A:K.478, A:K.478 Hydrogen bonds: A:K.478, A:K.478 LMR.9: 10 residues within 4Å: Chain B: N.24, S.25, R.27, I.148, G.212, G.213, R.216, R.267, R.298 Ligands: MG.6 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:N.24, B:S.25, B:G.213 Water bridges: B:D.20, B:D.20, B:D.20, B:N.24, B:S.25, B:D.147, B:G.150, B:R.267, B:R.267, B:R.267, B:R.267 Salt bridges: B:R.27, B:R.27, B:R.216, B:R.267, B:R.298

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

EDO.5: 5 residues within 4Å: Chain A: D.357, Y.360, P.431, S.432, T.435 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.357, A:S.432, A:T.435 EDO.10: 2 residues within 4Å: Chain B: K.384, Y.388 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.384, B:K.384

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.6: 2 residues within 4Å: Ligands: PO4.8, LMR.9 No protein-ligand interaction detected (PLIP)

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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