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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.402, A:K.403, A:T.404, A:T.404, A:T.404, 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:S.402, A:H.431, A:T.512 Salt bridges: A:H.431, A:R.511 FBP.6: 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 17 PLIP interactions: 17 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:T.432 Water bridges: B:H.431, B:T.512 Salt bridges: B:H.431, B:R.511 FBP.11: 10 residues within 4Å: Chain C: S.402, 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 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, C:V.510 Water bridges: C:T.512, C:T.512 Salt bridges: C:H.431, C:R.511 FBP.16: 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 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:S.402, D:K.403, D:T.404, 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 Water bridges: D:T.512, D:T.512 Salt bridges: D:H.431, D:R.511

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.270, D.294 Ligands: OXL.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.270, A:D.294, H2O.1, H2O.1 MG.7: 3 residues within 4Å: Chain B: E.270, D.294 Ligands: OXL.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.270, B:D.294, H2O.8, H2O.8 MG.12: 3 residues within 4Å: Chain C: E.270, D.294 Ligands: OXL.13 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.270, C:D.294, H2O.13, H2O.13 MG.17: 3 residues within 4Å: Chain D: E.270, D.294 Ligands: OXL.18 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.270, D:D.294, H2O.17, H2O.18

4 x OXL: OXALATE ION(Non-covalent)

OXL.3: 8 residues within 4Å: Chain A: K.268, E.270, A.291, R.292, G.293, D.294, T.326 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.293, A:D.294, A:D.294, A:T.326, A:T.326, A:T.326 Water bridges: A:R.74, A:K.268, A:K.268 Salt bridges: A:R.74, A:K.268 OXL.8: 8 residues within 4Å: Chain B: K.268, E.270, A.291, R.292, G.293, D.294, T.326 Ligands: MG.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.293, B:D.294, B:T.326, B:T.326, B:T.326 Water bridges: B:R.74, B:K.268 Salt bridges: B:R.74, B:K.268 OXL.13: 8 residues within 4Å: Chain C: K.268, E.270, A.291, R.292, G.293, D.294, T.326 Ligands: MG.12 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.270, C:E.270, C:G.293, C:D.294 Water bridges: C:K.268 Salt bridges: C:R.74, C:K.268, C:K.268 OXL.18: 8 residues within 4Å: Chain D: K.268, E.270, A.291, R.292, G.293, D.294, T.326 Ligands: MG.17 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.293, D:D.294, D:D.294 Water bridges: D:R.74, D:K.268, D:E.270, D:D.294 Salt bridges: D:R.74, D:K.268

4 x K: POTASSIUM ION(Non-covalent)

K.4: 6 residues within 4Å: Chain A: N.76, S.78, D.108, T.109, S.240, K.268 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.78, A:D.108, A:T.109, H2O.5 K.9: 6 residues within 4Å: Chain B: N.76, S.78, D.108, T.109, S.240, K.268 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.78, B:D.108, B:T.109, H2O.12 K.14: 6 residues within 4Å: Chain C: N.76, S.78, D.108, T.109, S.240, K.268 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.78, C:D.108, C:T.109 K.19: 6 residues within 4Å: Chain D: N.76, S.78, D.108, T.109, S.240, K.268 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:S.78, D:D.108, D:T.109

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 6 residues within 4Å: Chain A: K.93, G.233, I.234, N.235, L.453, R.456 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.233

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.10: 7 residues within 4Å: Chain B: K.93, F.105, G.233, I.234, N.235, L.453, R.456 No protein-ligand interaction detected (PLIP) PGE.15: 7 residues within 4Å: Chain C: K.93, G.233, I.234, N.235, E.452, L.453, R.456 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.235, C:E.452, C:R.456, C:R.456 PGE.20: 8 residues within 4Å: Chain D: K.93, F.105, G.233, I.234, N.235, E.452, L.453, R.456 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:I.234, D:R.456, D:R.456 Water bridges: D:N.235

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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