SMTL ID : 8iat.1

Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

8 x OXL: OXALATE ION(Non-covalent)

OXL.1: 8 residues within 4Å: Chain A: K.268, E.270, A.291, R.292, G.293, D.294, T.326 Ligands: MG.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.293, A:D.294, A:D.294, A:D.294 Water bridges: A:R.74, A:K.268 Salt bridges: A:R.74, A:K.268, A:K.268 OXL.2: 8 residues within 4Å: Chain A: T.427, K.428, T.429, H.431, T.432, G.507, E.508, A.509 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.427, A:K.428, A:T.429, A:H.431, A:T.432, A:T.432, A:G.507, A:A.509 Water bridges: A:T.429, A:G.503, A:V.510, A:V.510 Salt bridges: A:H.431 OXL.8: 8 residues within 4Å: Chain B: K.268, E.270, A.291, R.292, G.293, D.294, T.326 Ligands: MG.10 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.293, B:D.294, B:T.326, B:T.326 Water bridges: B:R.74, B:R.74, B:S.240, B:K.268 Salt bridges: B:K.268, B:K.268 OXL.9: 7 residues within 4Å: Chain B: T.427, K.428, T.429, H.431, T.432, R.511, T.512 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.427, B:K.428, B:T.429, B:T.432, B:T.432, B:T.512, B:T.512, B:T.512 Salt bridges: B:H.431 OXL.12: 8 residues within 4Å: Chain C: K.268, E.270, A.291, R.292, G.293, D.294, T.326 Ligands: MG.14 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.270, C:G.293, C:D.294 Water bridges: C:R.74, C:K.268 Salt bridges: C:R.74, C:K.268, C:K.268 OXL.13: 8 residues within 4Å: Chain C: T.427, K.428, T.429, H.431, T.432, G.507, E.508, A.509 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.428, C:T.429, C:H.431, C:T.432, C:G.507, C:A.509 OXL.17: 8 residues within 4Å: Chain D: K.268, E.270, A.291, R.292, G.293, D.294, T.326 Ligands: MG.19 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.293, D:D.294, D:T.326, D:T.326, D:T.326 Water bridges: D:R.74, D:K.268 Salt bridges: D:R.74, D:K.268, D:K.268 OXL.18: 7 residues within 4Å: Chain D: T.427, K.428, T.429, H.431, T.432, R.511, T.512 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:K.428, D:T.429, D:T.432, D:T.432, D:T.432, D:T.512 Salt bridges: D:H.431

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.270, D.294 Ligands: OXL.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.270, A:D.294, H2O.4, H2O.5 MG.10: 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.15, H2O.17 MG.14: 3 residues within 4Å: Chain C: E.270, D.294 Ligands: OXL.12 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.270, C:D.294, H2O.27, H2O.27 MG.19: 3 residues within 4Å: Chain D: E.270, D.294 Ligands: OXL.17 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.270, D:D.294, H2O.35, H2O.38

4 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: N.76, S.78, D.108, T.109, S.240 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.78, A:D.108, A:T.109, H2O.6, H2O.10 K.11: 6 residues within 4Å: Chain B: R.74, N.76, S.78, D.108, T.109, K.268 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.78, B:D.108, B:T.109, H2O.23, H2O.23 K.15: 6 residues within 4Å: Chain C: N.76, S.78, D.108, T.109, S.240, K.268 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.78, C:D.108, C:T.109, H2O.27, H2O.30 K.20: 6 residues within 4Å: Chain D: N.76, S.78, D.108, T.109, S.240, K.268 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.78, D:D.108, D:T.109, H2O.34, H2O.38

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 6 residues within 4Å: Chain A: Q.168, G.174, K.175, R.179, N.196 Chain D: R.337 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.168, A:R.179, A:R.179 Water bridges: A:N.196

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

PGE.6: 7 residues within 4Å: Chain A: K.93, F.105, G.233, I.234, N.235, L.453, R.456 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.235, A:R.456, A:R.456 PGE.16: 6 residues within 4Å: Chain C: Q.168, G.174, K.175, R.179, E.195, N.196 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.168, C:Q.168, C:K.175, C:R.179, C:R.179

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: T.30, R.74, N.76, H.79, S.360, G.361, A.364, N.365 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.74, A:R.74, A:N.76 Water bridges: A:N.76, A:S.78, A:S.360, A:S.360

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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