SMTL ID : 6pc0.1

Crystal structure of Helicobacter pylori PPX/GppA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

22 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 1 residues within 4Å: Chain A: R.103 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: K.140, K.206, N.207 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: L.381, A.382, H.383, K.415 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: R.225, F.246, K.249 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: K.14, K.32 Chain B: P.331, H.332 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain A: K.340, K.365 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: K.254, E.255, D.256 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: Q.36, R.308, N.309, H.310 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: P.331, H.332, E.333, K.334 Ligand excluded by PLIP SO4.10: 9 residues within 4Å: Chain A: G.22, S.23, N.24, S.25, R.27, G.149, G.150, G.151 Ligands: MLT.15 Ligand excluded by PLIP SO4.11: 6 residues within 4Å: Chain A: R.27, G.212, G.213, R.216, R.298 Ligands: MLT.15 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain B: K.359, Y.360, M.429, P.431 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain B: L.381, A.382, H.383, K.415 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain B: K.254, E.255, R.272 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain A: H.332 Chain B: K.14, K.32 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain B: K.416, I.417, P.418, K.419 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain B: K.191, E.248, M.252, L.276 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain B: N.317, K.340, K.365 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain B: K.341, K.345 Ligand excluded by PLIP SO4.24: 7 residues within 4Å: Chain B: N.24, S.25, R.27, K.46, G.213, R.216, R.267 Ligand excluded by PLIP SO4.25: 7 residues within 4Å: Chain B: G.22, S.23, N.24, S.25, R.27, G.149, G.150 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain B: R.216, A.217, K.220, N.264, R.267 Ligand excluded by PLIP

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

EDO.12: 5 residues within 4Å: Chain A: R.98, D.122, G.123, Q.124, S.168 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.98, A:G.123, A:Q.124 EDO.13: 5 residues within 4Å: Chain A: V.71, A.108, R.109, K.112, A.113 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.109 Water bridges: A:K.112 EDO.27: 6 residues within 4Å: Chain B: L.481, P.482, K.486, L.490, T.491, I.492 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.486, B:I.492 Water bridges: B:L.481, B:P.482 EDO.28: 4 residues within 4Å: Chain B: Q.124, L.166, I.167, S.168 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.124, B:S.168, B:S.168 EDO.29: 4 residues within 4Å: Chain A: Y.475 Chain B: I.65, Q.68, K.72 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.68 EDO.30: 2 residues within 4Å: Chain B: K.463, N.464 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.463, B:N.464 EDO.31: 4 residues within 4Å: Chain B: F.180, L.189, F.193 Ligands: EDO.33 No protein-ligand interaction detected (PLIP) EDO.32: 5 residues within 4Å: Chain B: F.226, D.227, Y.228, Y.236, M.426 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.226 EDO.33: 5 residues within 4Å: Chain B: F.180, K.183, L.185, L.189 Ligands: EDO.31 No protein-ligand interaction detected (PLIP)

2 x MLT: D-MALATE(Non-covalent)

MLT.14: 7 residues within 4Å: Chain A: L.330, H.332, H.335, S.336, S.372, K.375 Chain B: Y.84 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.335 Hydrogen bonds: A:H.335, A:S.372, A:S.372 Water bridges: A:H.332, A:H.335, A:K.375, A:K.375 Salt bridges: A:H.335, A:K.375 MLT.15: 11 residues within 4Å: Chain A: N.24, S.25, R.27, K.46, K.48, G.213, T.214, R.216, R.267 Ligands: SO4.10, SO4.11 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:N.24, A:S.25, A:S.25, A:G.213, A:T.214, A:T.214, A:R.216, A:R.267, A:R.267 Water bridges: A:K.46, A:K.46, A:K.48, A:T.214 Salt bridges: A:R.27, A:K.46, A:K.46, A:K.48, A:R.267, A:R.267

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

LMR.34: 5 residues within 4Å: Chain B: K.140, N.141, S.142, K.206, N.207 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.141, B:N.141, B:S.142, B:N.207 Water bridges: B:S.142 Salt bridges: B:K.140, B:K.206 LMR.35: 7 residues within 4Å: Chain A: Y.380 Chain B: S.232, L.233, H.234, G.294, S.395, R.403 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.234 Hydrogen bonds: B:L.233, B:H.234 Salt bridges: B:R.403 Water bridges: A:S.378

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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