SMTL ID : 8iax.1 (1 other biounit)

Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with phosphoenolpyruvate and fructose 1,6-bisphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)

FBP.1: 11 residues within 4Å: Chain A: S.402, K.403, T.404, T.427, K.428, T.429, G.430, H.431, T.432, V.510, R.511 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:S.402, A:K.403, A:T.404, A:T.404, A:T.427, A:T.427, A:T.427, A:K.428, A:T.429, A:G.430, A:H.431, A:T.432, A:T.432 Water bridges: A:R.511, A:T.512, A:T.512, A:T.512, A:T.512 Salt bridges: A:H.431, A:R.511 FBP.5: 11 residues within 4Å: Chain B: S.402, K.403, T.404, T.427, K.428, T.429, G.430, H.431, T.432, V.510, R.511 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:S.402, B:K.403, B:T.404, B:T.404, B:T.404, B:T.427, B:T.427, B:K.428, B:T.429, B:G.430, B:H.431, B:T.432, B:V.510 Water bridges: B:V.510, B:R.511, B:T.512 Salt bridges: B:H.431, B:R.511 FBP.9: 11 residues within 4Å: Chain C: S.402, K.403, T.404, T.427, K.428, T.429, G.430, H.431, T.432, V.510, R.511 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:S.402, C:K.403, C:T.404, C:T.404, C:T.404, C:T.427, C:T.427, C:T.427, C:K.428, C:T.429, C:G.430, C:H.431, C:T.432 Water bridges: C:K.428, C:K.428, C:V.510, C:R.511, C:T.512, C:T.512 Salt bridges: C:H.431, C:R.511 FBP.13: 11 residues within 4Å: Chain D: S.402, K.403, T.404, T.427, K.428, T.429, G.430, H.431, T.432, V.510, R.511 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:S.402, D:K.403, D:T.404, D:T.404, D:T.427, D:T.427, D:T.427, D:K.428, D:T.429, D:G.430, D:H.431, D:T.432, D:T.432 Water bridges: D:S.402, D:T.429, D:H.431, D:R.511, D:R.511, D:T.512, D:T.512, D:T.512, D:T.512 Salt bridges: D:H.431, D:R.511

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.2: 11 residues within 4Å: Chain A: R.74, K.268, E.270, A.291, R.292, G.293, D.294, T.326, M.358 Ligands: MG.3, K.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.291 Hydrogen bonds: A:G.293, A:D.294, A:T.326, A:T.326 Water bridges: A:N.76, A:N.76, A:E.113, A:K.268, A:K.268 Salt bridges: A:R.74, A:K.268 PEP.6: 12 residues within 4Å: Chain B: R.74, K.268, E.270, M.289, A.291, R.292, G.293, D.294, T.326, M.358 Ligands: MG.7, K.8 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:A.291 Hydrogen bonds: B:D.108, B:G.293, B:D.294, B:D.294, B:D.294 Water bridges: B:N.76, B:N.76, B:S.240, B:K.268, B:K.268, B:S.360 Salt bridges: B:R.74, B:K.268 PEP.10: 13 residues within 4Å: Chain C: R.74, D.108, K.268, E.270, M.289, A.291, R.292, G.293, D.294, T.326, M.358 Ligands: MG.11, K.12 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:A.291 Hydrogen bonds: C:G.293, C:D.294, C:D.294 Water bridges: C:N.76, C:S.78, C:S.240, C:K.268, C:K.268 Salt bridges: C:R.74, C:K.268 PEP.14: 13 residues within 4Å: Chain D: R.74, D.108, K.268, E.270, M.289, A.291, R.292, G.293, D.294, T.326, M.358 Ligands: MG.15, K.16 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:D.108, D:G.293, D:D.294, D:T.326, D:T.326 Water bridges: D:N.76, D:S.78, D:K.268, D:K.268, D:S.360, D:S.360 Salt bridges: D:R.74, D:K.268

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.270, D.294 Ligands: PEP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.270, A:D.294, H2O.6 MG.7: 3 residues within 4Å: Chain B: E.270, D.294 Ligands: PEP.6 4 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:E.270, B:D.294, PEP.6, H2O.16 MG.11: 3 residues within 4Å: Chain C: E.270, D.294 Ligands: PEP.10 4 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: C:E.270, C:D.294, PEP.10, H2O.29 MG.15: 3 residues within 4Å: Chain D: E.270, D.294 Ligands: PEP.14 4 PLIP interactions: 2 interactions with chain D, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: D:E.270, D:D.294, PEP.14, H2O.46

4 x K: POTASSIUM ION(Non-covalent)

K.4: 7 residues within 4Å: Chain A: N.76, S.78, D.108, T.109, S.240, K.268 Ligands: PEP.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:S.78, A:D.108, A:T.109, PEP.2 K.8: 7 residues within 4Å: Chain B: N.76, S.78, D.108, T.109, S.240, K.268 Ligands: PEP.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.78, B:D.108, B:T.109, H2O.16 K.12: 7 residues within 4Å: Chain C: N.76, S.78, D.108, T.109, S.240, K.268 Ligands: PEP.10 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.78, C:D.108, C:T.109 K.16: 6 residues within 4Å: Chain D: N.76, S.78, D.108, T.109, S.240 Ligands: PEP.14 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:S.78, D:D.108, D:T.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Taguchi, A. et al., Functional and structural characterization of Streptococcus pneumoniae pyruvate kinase involved in fosfomycin resistance. J.Biol.Chem. (2023)

Release Date

2023-06-14

Peptides

Pyruvate kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase

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