SMTL ID : 6wp5.1

Pyruvate Kinase M2 mutant-S37D

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 6 residues within 4Å: Chain A: R.92, N.94, S.96, D.132, K.289 Ligands: OXL.7 No protein-ligand interaction detected (PLIP) K.9: 7 residues within 4Å: Chain B: N.94, S.96, D.132, T.133, E.137, S.262, K.289 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.96 K.14: 3 residues within 4Å: Chain C: T.69, R.92, N.94 No protein-ligand interaction detected (PLIP) K.15: 7 residues within 4Å: Chain C: N.94, S.96, D.132, T.133, E.137, S.262, K.289 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.132, C:T.133

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: T.69, R.92, N.94, S.381, G.382, A.385 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.92, A:N.94 GOL.3: 11 residues within 4Å: Chain A: R.62, N.63, T.64, G.65, N.89, H.483, Y.485, G.487, I.488, F.489 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.89, A:Y.485, A:G.487, A:I.488, A:I.488 GOL.4: 6 residues within 4Å: Chain A: T.60, A.61, R.62, H.398, F.489 Ligands: GOL.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.60, A:R.62, A:R.62 GOL.5: 8 residues within 4Å: Chain A: L.450, T.451, K.452, W.501, R.508, P.536, G.537 Ligands: FBP.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.508, A:G.537 GOL.10: 6 residues within 4Å: Chain B: P.136, N.229, L.230, F.263, R.265, E.319 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.136, B:L.230, B:R.265, B:R.265, B:E.319, B:E.319 GOL.11: 7 residues within 4Å: Chain B: T.451, K.452, S.453, G.454, R.455, S.456, T.541 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.451, B:K.452, B:S.453, B:S.453, B:G.454, B:S.456, B:S.456, B:T.541 GOL.16: 9 residues within 4Å: Chain C: R.62, N.63, G.65, N.89, H.483, Y.485, G.487, I.488, F.489 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.63, C:N.89, C:H.483, C:G.487 GOL.17: 8 residues within 4Å: Chain C: P.136, I.138, V.228, N.229, L.230, V.235, R.265, E.319 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:P.136, C:L.230, C:R.265, C:E.319 GOL.21: 2 residues within 4Å: Chain D: W.501, G.539 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.539, D:G.539

3 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: E.291, D.315 Ligands: OXL.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.291, A:D.315, H2O.1, H2O.2 MG.12: 3 residues within 4Å: Chain B: E.291, D.315 Ligands: OXL.13 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.291, B:D.315 MG.18: 3 residues within 4Å: Chain C: E.291, D.315 Ligands: OXL.19 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.291, C:D.315, H2O.5, H2O.5

4 x OXL: OXALATE ION(Non-covalent)

OXL.7: 9 residues within 4Å: Chain A: K.289, E.291, A.312, R.313, G.314, D.315, T.347 Ligands: K.1, MG.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.291, A:G.314, A:D.315 Water bridges: A:K.289 Salt bridges: A:R.92, A:K.289, A:K.289 OXL.13: 8 residues within 4Å: Chain B: K.289, E.291, A.312, R.313, G.314, D.315, T.347 Ligands: MG.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.291, B:G.314, B:D.315 Salt bridges: B:R.92, B:K.289, B:K.289 OXL.19: 9 residues within 4Å: Chain C: K.289, E.291, M.310, A.312, R.313, G.314, D.315, T.347 Ligands: MG.18 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.314, C:D.315, C:T.347, C:T.347, C:T.347 Water bridges: C:K.289 Salt bridges: C:R.92, C:K.289 OXL.22: 7 residues within 4Å: Chain D: K.289, E.291, A.312, R.313, G.314, D.315, T.347 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.314, D:D.315, D:D.315, D:T.347, D:T.347 Salt bridges: D:K.289

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

FBP.8: 9 residues within 4Å: Chain A: T.451, K.452, S.453, G.454, R.455, S.456, S.538, G.539 Ligands: GOL.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.451, A:K.452, A:S.453, A:G.454, A:R.455, A:S.456, A:S.456, A:S.456, A:G.537, A:S.538, A:G.539 FBP.20: 9 residues within 4Å: Chain C: T.451, K.452, S.453, G.454, R.455, S.456, G.537, S.538, G.539 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.451, C:K.452, C:S.453, C:G.454, C:S.456, C:S.456, C:G.539 FBP.23: 6 residues within 4Å: Chain D: T.451, K.452, S.453, G.454, R.455, S.456 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.451, D:T.451, D:K.452, D:S.453, D:G.454, D:S.456, D:S.456

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nandi, S. et al., Structural basis for allosteric regulation of pyruvate kinase M2 by phosphorylation and acetylation. J.Biol.Chem. (2020)

Release Date

2020-09-30

Peptides

Pyruvate kinase PKM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
D

Pyruvate kinase PKM