SMTL ID : 7fs6.1 (1 other biounit)

Structure of liver pyruvate kinase in complex with allosteric modulator 18

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 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 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:T.348, A:T.349, A:T.350, A:G.351, A:S.353, A:S.353, A:G.430, A:R.432, A:R.432, A:G.434, A:S.435, A:G.436, A:Y.437 Water bridges: A:R.371, A:R.405, A:T.438, A:T.438 Salt bridges: A:R.405 FBP.6: 17 residues within 4Å: Chain B: L.347, T.348, T.349, T.350, G.351, R.352, S.353, W.398, R.405, G.430, R.432, P.433, G.434, S.435, G.436, Y.437, T.438 17 PLIP interactions: 17 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.405, B:R.405 Salt bridges: B:R.405 FBP.12: 16 residues within 4Å: Chain C: 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 C Hydrogen bonds: C:T.348, C:T.348, C:T.349, 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:R.352, C:R.352, C:R.405, C:R.405, C:S.435 Salt bridges: C:R.405 FBP.17: 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 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:T.348, D:T.349, D:T.350, D:G.351, 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:T.349, D:T.350, D:R.352, D:R.405, D:R.405, D:T.438 Salt bridges: D:R.405

4 x OXL: OXALATE ION(Non-covalent)

OXL.2: 8 residues within 4Å: Chain A: K.186, E.188, A.209, R.210, G.211, D.212, T.244 Ligands: MG.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.211, A:D.212, A:T.244, A:T.244, A:T.244 Salt bridges: A:R.87, A:K.186, A:K.186 OXL.7: 10 residues within 4Å: Chain B: K.186, E.188, A.209, R.210, G.211, D.212, T.244 Ligands: MG.8, K.9, Y3Z.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.211, B:D.212 Salt bridges: B:R.87, B:K.186, B:K.186 OXL.13: 8 residues within 4Å: Chain C: K.186, E.188, A.209, R.210, G.211, D.212, T.244 Ligands: MG.14 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.211, C:D.212 Water bridges: C:K.186 Salt bridges: C:R.87, C:K.186, C:K.186 OXL.18: 9 residues within 4Å: Chain D: K.186, E.188, A.209, R.210, G.211, D.212, T.244 Ligands: MG.19, Y3Z.21 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.211, D:D.212, D:T.244, D:T.244, D:T.244 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: OXL.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.188, A:D.212 MG.8: 5 residues within 4Å: Chain B: K.186, E.188, D.212 Ligands: OXL.7, Y3Z.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.188, B:D.212, H2O.4 MG.14: 3 residues within 4Å: Chain C: E.188, D.212 Ligands: OXL.13 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.188, C:D.212, H2O.12 MG.19: 4 residues within 4Å: Chain D: K.186, E.188, D.212 Ligands: OXL.18 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.188, D:E.188, D:D.212

4 x K: POTASSIUM ION(Non-covalent)

K.4: 6 residues within 4Å: Chain A: N.89, S.91, D.127, T.128, S.159, K.186 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.91, A:T.128 K.9: 7 residues within 4Å: Chain B: N.89, S.91, D.127, T.128, S.159, K.186 Ligands: OXL.7 No protein-ligand interaction detected (PLIP) K.15: 6 residues within 4Å: Chain C: N.89, S.91, D.127, T.128, S.159, K.186 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.91, C:D.127, C:T.128 K.20: 6 residues within 4Å: Chain D: N.89, S.91, D.127, T.128, S.159, K.186 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:S.91, D:D.127, D:T.128

6 x Y3Z: (10aM)-6-{2-[4-(3,4-dihydroxybenzene-1-sulfonyl)phenyl]ethyl}-2,3,8,9-tetrahydroxy-5lambda~6~-dibenzo[c,e][1,2]thiazine-5,5(6H)-dione(Non-covalent)

Y3Z.5: 20 residues within 4Å: Chain A: F.40, L.41, L.44, K.227, L.269, D.270, Y.306, Q.309, L.310, E.313 Chain C: F.40, L.41, L.44, N.234, L.269, D.270, Y.306, Q.309, L.310, E.313 15 PLIP interactions: 6 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: C:F.40, C:L.44, C:L.310, A:F.40, A:L.310 Hydrogen bonds: C:E.313, C:E.313, A:L.41, A:K.227, A:Y.306, A:E.313, A:E.313 pi-Stacking: C:F.40, A:F.40, A:F.40 Y3Z.10: 12 residues within 4Å: Chain B: N.89, H.92, G.211, D.212, I.215, T.244, Q.245, S.278 Chain D: R.258 Ligands: OXL.7, MG.8, Y3Z.11 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.215, B:T.244 Hydrogen bonds: B:D.212, B:S.278, B:S.278 Y3Z.11: 9 residues within 4Å: Chain B: H.92, Q.245, E.248, I.251, S.278, G.279, A.282, K.283 Ligands: Y3Z.10 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.251 Hydrogen bonds: B:E.248, B:G.279 Water bridges: B:Q.245, B:S.278 Y3Z.16: 19 residues within 4Å: Chain B: F.40, L.41, L.44, L.269, D.270, Y.306, Q.309, L.310, E.313 Chain D: F.40, L.41, L.44, L.269, D.270, V.305, Y.306, Q.309, L.310, E.313 15 PLIP interactions: 4 interactions with chain B, 11 interactions with chain D Hydrophobic interactions: B:F.40, B:L.44, D:F.40, D:L.44, D:L.310 pi-Stacking: B:F.40, B:F.40, D:F.40, D:F.40 Hydrogen bonds: D:D.270, D:Y.306, D:E.313 Water bridges: D:K.227, D:K.227, D:K.227 Y3Z.21: 14 residues within 4Å: Chain B: R.258 Chain D: R.87, N.89, S.91, H.92, G.211, D.212, I.215, T.244, Q.245, E.248, S.278 Ligands: OXL.18, Y3Z.22 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:I.215 Hydrogen bonds: D:S.91, D:S.278 pi-Stacking: D:H.92 Water bridges: B:R.258 Y3Z.22: 8 residues within 4Å: Chain D: H.92, Q.245, E.248, I.251, S.278, G.279, K.283 Ligands: Y3Z.21 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.251, D:K.283 Hydrogen bonds: D:H.92, D:E.248, D:G.279, D:K.283 Water bridges: D:Q.245, D:S.278

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nain-Perez, A. et al., Tuning liver pyruvate kinase activity up or down with a new class of allosteric modulators. Eur.J.Med.Chem. (2023)

Release Date

2023-04-12

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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