SMTL ID : 6qxl.1 (2 other biounits)

Crystal Structure of Pyruvate Kinase II (PykA) from Pseudomonas aeruginosa in complex with sodium malonate, magnesium and glucose-6-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

homo-tetramer

Ligands

4 x G6P: 6-O-phosphono-alpha-D-glucopyranose(Non-covalent)

G6P.1: 16 residues within 4Å: Chain A: L.383, T.384, E.385, S.386, G.387, F.388, T.389, G.461, D.462, S.463, Y.464, A.466, Q.467, G.468, G.469, T.470 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.384, A:T.384, A:T.384, A:E.385, A:E.385, A:S.386, A:G.387, A:F.388, A:T.389, A:T.389, A:G.461, A:S.463, A:G.468, A:G.469, A:G.469 Water bridges: A:T.470, A:T.470 G6P.4: 17 residues within 4Å: Chain B: L.383, T.384, E.385, S.386, G.387, F.388, T.389, K.460, G.461, D.462, S.463, Y.464, A.466, Q.467, G.468, G.469, T.470 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:L.383, B:E.385, B:S.386, B:G.387, B:F.388, B:T.389, B:G.461, B:S.463, B:G.468, B:G.469, B:G.469, B:T.470 Water bridges: B:T.384, B:T.384, B:D.462, B:S.463 G6P.8: 17 residues within 4Å: Chain C: L.383, T.384, E.385, S.386, G.387, F.388, T.389, K.460, G.461, D.462, S.463, Y.464, A.466, Q.467, G.468, G.469, T.470 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:E.385, C:S.386, C:G.387, C:F.388, C:T.389, C:G.461, C:G.461, C:G.468, C:G.469 Water bridges: C:D.360, C:D.360, C:Q.467, C:T.470 G6P.11: 15 residues within 4Å: Chain D: L.383, T.384, E.385, S.386, G.387, F.388, T.389, G.461, D.462, S.463, A.466, Q.467, G.468, G.469, T.470 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:T.384, D:T.384, D:T.384, D:E.385, D:E.385, D:S.386, D:G.387, D:F.388, D:T.389, D:T.389, D:G.461, D:S.463, D:G.468, D:G.469 Water bridges: D:T.384, D:T.384, D:S.463, D:Q.467

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.223, D.250 Ligands: MLI.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.223, A:D.250, H2O.1, H2O.3 MG.5: 3 residues within 4Å: Chain B: E.223, D.250 Ligands: MLI.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.223, B:D.250 MG.9: 3 residues within 4Å: Chain C: E.223, D.250 Ligands: MLI.10 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.223, C:D.250 MG.12: 4 residues within 4Å: Chain D: K.221, E.223, D.250 Ligands: MLI.13 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.223, D:D.250

4 x MLI: MALONATE ION(Non-functional Binders)

MLI.3: 9 residues within 4Å: Chain A: R.34, K.221, E.223, A.247, R.248, G.249, D.250, T.282 Ligands: MG.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.247 Hydrogen bonds: A:G.249, A:D.250, A:T.282, A:T.282 Water bridges: A:K.73, A:T.282, A:S.316 Salt bridges: A:R.34, A:K.221 MLI.7: 9 residues within 4Å: Chain B: R.34, K.221, E.223, A.247, R.248, G.249, D.250, T.282 Ligands: MG.5 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.247 Hydrogen bonds: B:E.223, B:G.249, B:D.250 Salt bridges: B:R.34, B:K.221 MLI.10: 9 residues within 4Å: Chain C: R.34, K.221, E.223, A.247, R.248, G.249, D.250, T.282 Ligands: MG.9 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:A.247 Hydrogen bonds: C:E.223, C:G.249, C:D.250 Water bridges: C:N.36 Salt bridges: C:R.34, C:K.221 MLI.13: 9 residues within 4Å: Chain D: R.34, K.221, E.223, A.247, R.248, G.249, D.250, T.282 Ligands: MG.12 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:A.247 Hydrogen bonds: D:G.249, D:D.250, D:T.282, D:T.282 Water bridges: D:R.34, D:S.194 Salt bridges: D:R.34, D:K.221

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain B: W.217, S.241, D.242, K.276, F.388, L.391 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.242 Water bridges: B:K.276, B:K.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abdelhamid, Y. et al., Evolutionary plasticity in the allosteric regulator-binding site of pyruvate kinase isoform PykA fromPseudomonas aeruginosa. J.Biol.Chem. (2019)

Release Date

2019-09-11

Peptides

Pyruvate kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
G

D
H

Pyruvate kinase

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