SMTL ID : 8iaw.1

Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with phosphoenolpyruvate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.270, D.294 Ligands: PEP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.270, A:D.294 MG.6: 3 residues within 4Å: Chain B: E.270, D.294 Ligands: PEP.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.270, B:D.294, PEP.7 MG.11: 3 residues within 4Å: Chain C: E.270, D.294 Ligands: PEP.12 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.270, C:D.294 MG.16: 3 residues within 4Å: Chain D: E.270, D.294 Ligands: PEP.17 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:E.270, D:D.294, PEP.17

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.2: 9 residues within 4Å: Chain A: R.74, K.268, E.270, A.291, R.292, G.293, D.294, T.326 Ligands: MG.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.291 Hydrogen bonds: A:N.76, A:G.293, A:D.294 Salt bridges: A:R.74, A:K.268 PEP.7: 9 residues within 4Å: Chain B: R.74, K.268, E.270, A.291, R.292, G.293, D.294, T.326 Ligands: MG.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.291 Hydrogen bonds: B:G.293, B:D.294, B:T.326, B:T.326 Salt bridges: B:R.74, B:K.268 PEP.12: 9 residues within 4Å: Chain C: R.74, K.268, E.270, A.291, R.292, G.293, D.294, T.326 Ligands: MG.11 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.291 Hydrogen bonds: C:N.76, C:G.293, C:D.294 Salt bridges: C:R.74, C:K.268 PEP.17: 9 residues within 4Å: Chain D: R.74, K.268, E.270, A.291, R.292, G.293, D.294, T.326 Ligands: MG.16 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:A.291 Hydrogen bonds: D:G.293, D:D.294, D:T.326, D:T.326 Salt bridges: D:R.74, D:K.268

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

SO4.3: 8 residues within 4Å: Chain A: L.426, T.427, K.428, T.429, G.430, H.431, T.432, R.511 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.427, A:T.427, A:K.428, A:T.429, A:G.430, A:H.431, A:T.432 Salt bridges: A:R.511 SO4.4: 5 residues within 4Å: Chain A: L.468, T.469, D.470, R.484, K.485 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.469, A:D.470 Salt bridges: A:R.484, A:K.485 SO4.5: 7 residues within 4Å: Chain A: R.516, I.517, R.518, T.519, R.521 Chain B: K.403, N.513 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.519, B:N.513 Salt bridges: A:R.516, A:R.518, A:R.521, B:K.403 SO4.8: 8 residues within 4Å: Chain A: K.403, V.510, N.513 Chain B: R.516, I.517, R.518, T.519, R.521 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:N.513, B:T.519, B:T.519 Salt bridges: A:K.403, B:R.516, B:R.518, B:R.521 SO4.9: 7 residues within 4Å: Chain B: T.427, K.428, T.429, G.430, H.431, T.432, V.510 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.427, B:K.428, B:T.429, B:G.430, B:H.431, B:T.432, B:T.432 Water bridges: B:G.503 SO4.10: 4 residues within 4Å: Chain B: T.469, D.470, R.484, K.485 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.469, B:D.470, B:D.470, B:D.470 Salt bridges: B:R.484, B:K.485 SO4.13: 8 residues within 4Å: Chain C: L.426, T.427, K.428, T.429, G.430, H.431, T.432, R.511 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.427, C:T.427, C:K.428, C:T.429, C:G.430, C:H.431, C:T.432 Salt bridges: C:R.511 SO4.14: 5 residues within 4Å: Chain C: L.468, T.469, D.470, R.484, K.485 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.469, C:D.470 Salt bridges: C:R.484, C:K.485 SO4.15: 7 residues within 4Å: Chain C: R.516, I.517, R.518, T.519, R.521 Chain D: K.403, N.513 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:T.519, D:N.513 Salt bridges: C:R.516, C:R.518, C:R.521, D:K.403 SO4.18: 8 residues within 4Å: Chain C: K.403, V.510, N.513 Chain D: R.516, I.517, R.518, T.519, R.521 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:T.519, D:T.519, C:N.513 Salt bridges: D:R.516, D:R.518, D:R.521, C:K.403 SO4.19: 7 residues within 4Å: Chain D: T.427, K.428, T.429, G.430, H.431, T.432, V.510 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.427, D:K.428, D:T.429, D:G.430, D:H.431, D:T.432, D:T.432 Water bridges: D:G.503 SO4.20: 4 residues within 4Å: Chain D: T.469, D.470, R.484, K.485 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.469, D:D.470, D:D.470, D:D.470 Salt bridges: D:R.484, D:K.485

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
A

D
B

Pyruvate kinase

Related Entries With Identical Sequence