SMTL ID : 7qdn.1 (1 other biounit)

Structure of human liver pyruvate kinase from which the B domain has been deleted

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

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

FBP.1: 16 residues within 4Å: Chain A: L.347, T.348, T.349, T.350, R.352, S.353, W.398, R.405, G.430, R.432, P.433, G.434, S.435, G.436, Y.437, T.438 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:T.348, A:T.349, A:T.350, A:S.353, A:S.353, A:G.430, A:R.432, A:G.434, A:S.435, A:G.436, A:Y.437 Water bridges: A:T.349, A:R.371, A:R.371, A:R.405, A:R.405, A:R.405, A:R.405, A:T.438 Salt bridges: A:R.405 FBP.5: 16 residues within 4Å: Chain B: L.347, T.348, T.349, T.350, R.352, S.353, W.398, R.405, G.430, R.432, P.433, G.434, S.435, G.436, Y.437, T.438 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:T.348, B:T.349, B:T.349, B:T.350, B:G.351, B:S.353, B:S.353, B:G.430, B:R.432, B:R.432, B:G.434, B:G.436, B:Y.437 Water bridges: B:L.347, B:R.371, B:R.405, B:R.405, B:R.405, B:G.430, B:T.438 Salt bridges: B:R.405 FBP.10: 17 residues within 4Å: Chain C: L.347, T.348, T.349, T.350, R.352, S.353, W.398, R.405, T.429, G.430, R.432, P.433, G.434, S.435, G.436, Y.437, T.438 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:T.348, C:T.348, C:T.349, C:T.350, C:G.351, C:S.353, C:S.353, C:G.430, C:R.432, C:R.432, C:G.434, C:G.436, C:Y.437 Water bridges: C:L.347, C:L.347, C:T.349, C:T.349, C:R.405, C:G.430 Salt bridges: C:R.405 FBP.15: 16 residues within 4Å: Chain D: L.347, T.348, T.349, T.350, R.352, S.353, W.398, R.405, G.430, R.432, P.433, G.434, S.435, G.436, Y.437, T.438 23 PLIP interactions: 23 interactions with chain D Hydrogen bonds: D:T.348, D:T.349, D:T.350, D:G.351, D:S.353, D:S.353, D:G.430, D:R.432, D:R.432, D:G.434, D:S.435, D:G.436, D:Y.437 Water bridges: D:L.347, D:T.349, D:T.349, D:W.398, D:D.401, D:R.405, D:R.405, D:G.430, D:T.438 Salt bridges: D:R.405

4 x OXD: OXALIC ACID(Non-covalent)

OXD.2: 8 residues within 4Å: Chain A: K.186, E.188, A.209, R.210, G.211, D.212, T.244 Ligands: MG.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.211, A:D.212, A:D.212, A:T.244, A:T.244, A:T.244 Water bridges: A:R.87, A:R.87, A:K.186, A:K.186 Salt bridges: A:R.87, A:K.186, A:K.186 OXD.6: 9 residues within 4Å: Chain B: R.87, K.186, E.188, A.209, R.210, G.211, D.212, T.244 Ligands: MG.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.211, B:D.212, B:D.212, B:D.212 Water bridges: B:R.87, B:K.186, B:K.186 Salt bridges: B:R.87, B:K.186, B:K.186 OXD.11: 8 residues within 4Å: Chain C: K.186, E.188, A.209, R.210, G.211, D.212, T.244 Ligands: MG.12 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.211, C:D.212, C:D.212 Water bridges: C:R.87, C:K.186, C:E.188, C:D.212 Salt bridges: C:R.87, C:K.186, C:K.186 OXD.16: 9 residues within 4Å: Chain D: R.87, K.186, E.188, A.209, R.210, G.211, D.212, T.244 Ligands: MG.17 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:E.188, D:G.211, D:D.212, D:T.244, D:T.244, D:T.244 Water bridges: D:R.87 Salt bridges: D:R.87, D:K.186, D:K.186

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.188, D.212 Ligands: OXD.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.188, A:D.212, H2O.1, H2O.2 MG.7: 3 residues within 4Å: Chain B: E.188, D.212 Ligands: OXD.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.188, B:D.212, H2O.13, H2O.15 MG.12: 3 residues within 4Å: Chain C: E.188, D.212 Ligands: OXD.11 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.188, C:D.212, H2O.20, H2O.23 MG.17: 3 residues within 4Å: Chain D: E.188, D.212 Ligands: OXD.16 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.188, D:D.212, H2O.37, H2O.38

4 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: N.89, S.91, D.127, T.128, S.159 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.91, A:D.127, A:T.128, H2O.3 K.8: 6 residues within 4Å: Chain B: N.89, S.91, D.127, T.128, S.159, K.186 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.91, B:D.127, B:T.128, H2O.14, H2O.18 K.13: 5 residues within 4Å: Chain C: N.89, S.91, D.127, T.128, S.159 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.91, C:D.127, C:T.128, H2O.26, H2O.29 K.18: 5 residues within 4Å: Chain D: N.89, S.91, D.127, T.128, S.159 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.91, D:D.127, D:T.128, H2O.36, H2O.44

3 x NA: SODIUM ION(Non-functional Binders)

NA.9: 7 residues within 4Å: Chain B: S.58, S.60, V.379, H.380, C.382, G.384, V.385 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.380, B:G.384, B:V.385 NA.14: 5 residues within 4Å: Chain C: S.58, T.59, S.60, H.380, C.382 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:C.382, C:G.384 Water bridges: C:S.60 NA.19: 4 residues within 4Å: Chain D: S.58, T.59, S.60, H.380 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:C.382, D:G.384 Water bridges: D:S.60, D:H.380

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nain-Perez, A. et al., Anthraquinone derivatives as ADP-competitive inhibitors of liver pyruvate kinase. Eur.J.Med.Chem. (2022)

Release Date

2022-03-30

Peptides

Pyruvate kinase PKLR: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase PKLR

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