SMTL ID : 8xw9.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

6 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 1 residues within 4Å: Ligands: UDP.6 No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain A: E.270, D.294 Ligands: OXL.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.270, A:D.294, H2O.3, H2O.8 MG.7: 3 residues within 4Å: Chain B: E.270, D.294 Ligands: OXL.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.270, B:D.294, H2O.25, H2O.25 MG.11: 1 residues within 4Å: Ligands: UDP.16 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain C: E.270, D.294 Ligands: OXL.14 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.270, C:D.294, H2O.38, H2O.43 MG.17: 3 residues within 4Å: Chain D: E.270, D.294 Ligands: OXL.19 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.270, D:D.294, H2O.60, H2O.60

4 x K: POTASSIUM ION(Non-covalent)

K.3: 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.9, H2O.13 K.8: 5 residues within 4Å: Chain B: N.76, S.78, D.108, T.109, S.240 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.78, B:D.108, B:T.109, H2O.24, H2O.32 K.13: 5 residues within 4Å: Chain C: N.76, S.78, D.108, T.109, S.240 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.78, C:D.108, C:T.109, H2O.44, H2O.48 K.18: 5 residues within 4Å: Chain D: N.76, S.78, D.108, T.109, S.240 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.78, D:D.108, D:T.109, H2O.59, H2O.67

4 x OXL: OXALATE ION(Non-covalent)

OXL.4: 8 residues within 4Å: Chain A: K.268, E.270, A.291, R.292, G.293, D.294, T.326 Ligands: MG.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.293, A:D.294, A:T.326, A:T.326 Water bridges: A:R.74, A:R.74, A:R.74, A:K.268 Salt bridges: A:R.74, A:K.268 OXL.9: 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 Salt bridges: B:R.74, B:K.268, B:K.268 OXL.14: 8 residues within 4Å: Chain C: K.268, E.270, A.291, R.292, G.293, D.294, T.326 Ligands: MG.12 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.293, C:D.294, C:T.326, C:T.326, C:T.326 Water bridges: C:R.74, C:R.74, C:R.74, C:K.268 Salt bridges: C:R.74, C:K.268 OXL.19: 8 residues within 4Å: Chain D: K.268, E.270, A.291, R.292, G.293, D.294, T.326 Ligands: MG.17 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.293, D:D.294, D:T.326, D:T.326 Water bridges: D:R.74 Salt bridges: D:R.74, D:K.268, D:K.268

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

FBP.5: 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.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:T.512, A:T.512, A:T.512, A:T.512 Salt bridges: A:H.431, A:R.511 FBP.10: 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 20 PLIP interactions: 20 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:S.402, B:H.431, B:V.510, B:V.510, B:T.512 Salt bridges: B:H.431, B:R.511 FBP.15: 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 17 PLIP interactions: 17 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:K.428, C:T.429, C:G.430, C:H.431, C:T.432 Water bridges: C:T.512, C:T.512, C:T.512 Salt bridges: C:H.431, C:R.511 FBP.20: 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 23 PLIP interactions: 23 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:S.402, D:H.431, D:V.510, D:V.510, D:T.512, D:T.512, D:T.512, D:T.512 Salt bridges: D:H.431, D:R.511

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.6: 14 residues within 4Å: Chain A: T.30, L.31, P.33, R.74, N.76, H.79, R.88, R.115, K.204, S.360, G.361, A.364, N.365 Ligands: MG.1 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.76, A:H.79, A:R.88, A:K.204, A:N.365 Water bridges: A:R.74, A:R.74, A:R.74, A:Q.85, A:R.88, A:D.172, A:S.360, A:G.361, A:N.365 Salt bridges: A:R.74, A:H.79, A:R.115 pi-Stacking: A:H.79 UDP.16: 14 residues within 4Å: Chain C: T.30, L.31, P.33, R.74, N.76, H.79, R.88, R.115, K.204, S.360, G.361, A.364, N.365 Ligands: MG.11 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:N.76, C:H.79, C:R.88, C:K.204, C:S.360, C:N.365 Water bridges: C:R.74, C:R.74, C:R.74, C:H.79, C:Q.85, C:R.88, C:R.115, C:S.360, C:G.361, C:N.365 Salt bridges: C:R.74, C:H.79, C:R.115 pi-Stacking: C:H.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Taguchi, A. et al., Structural Basis of Nucleotide Selectivity in Pyruvate Kinase. J.Mol.Biol. (2024)

Release Date

2024-07-31

Peptides

Pyruvate kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Pyruvate kinase

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