SMTL ID : 6pc1.2 (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 MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 2 residues within 4Å: Chain A: E.126 Ligands: PO4.3 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: G4P.2 No protein-ligand interaction detected (PLIP)

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

G4P.2: 14 residues within 4Å: Chain A: R.27, E.44, K.46, R.216, K.220, L.233, H.234, N.264, R.267, G.294 Chain B: Y.380, L.381, K.415 Ligands: MG.5 23 PLIP interactions: 5 interactions with chain B, 18 interactions with chain A Hydrogen bonds: B:L.381, A:K.220, A:K.220, A:H.234, A:N.264, A:G.294, A:G.294 Water bridges: B:A.382, A:R.216, A:L.233, A:L.233, A:R.298 Salt bridges: B:K.415, A:R.27, A:E.44, A:K.46, A:K.46, A:R.216, A:K.220, A:K.220, A:R.267 pi-Stacking: B:Y.380, B:Y.380 G4P.7: 11 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, R.267, G.294 18 PLIP interactions: 13 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:K.220, B:K.220, B:N.264, B:G.294, B:G.294, A:L.381 Water bridges: B:L.233, B:R.298, A:A.382 Salt bridges: B:R.27, B:E.44, B:K.46, B:R.216, B:K.220, B:R.267, A:K.415 pi-Stacking: A:Y.380, A:Y.380

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

PO4.3: 10 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.1 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.23, A:S.23, A:T.94, A:S.95, A:G.150, A:G.151, A:S.152, A:S.152, A:S.152 Water bridges: A:N.24, A:E.126, A:E.126, A:G.149, A:G.149 PO4.6: 2 residues within 4Å: Chain A: K.188, K.191 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.191 PO4.8: 8 residues within 4Å: Chain B: S.23, T.94, S.95, E.126, G.149, G.150, G.151, S.152 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.23, B:T.94, B:T.94, B:T.94, B:S.95, B:G.150, B:G.151, B:S.152 Water bridges: B:E.126, B:E.126

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

LMR.4: 10 residues within 4Å: Chain A: D.20, N.24, S.25, R.27, I.148, G.212, G.213, R.216, R.267, R.298 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:D.20, A:N.24, A:S.25, A:G.213 Water bridges: A:N.24, A:D.147, A:D.147, A:G.150, A:T.214, A:R.298, A:R.298 Salt bridges: A:R.27, A:R.216, A:R.267, A:R.298 LMR.9: 8 residues within 4Å: Chain B: N.24, S.25, R.27, G.212, G.213, R.216, R.267, R.298 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.20, B:N.24, B:G.213 Water bridges: B:S.25, B:R.267 Salt bridges: B:R.27, B:R.216, B:R.267, B:R.298

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
C

B
D

Guanosine pentaphosphate phosphohydrolase

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