SMTL ID : 6wp6.1

Pyruvate Kinase M2 mutant-S37E K433E

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-tetramer

Ligands

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.1: 7 residues within 4Å: Chain A: T.451, E.452, S.453, G.454, R.455, S.456, T.541 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.452, A:S.453, A:G.454, A:R.455, A:S.456 NO3.8: 7 residues within 4Å: Chain C: T.451, E.452, S.453, G.454, R.455, S.456, T.541 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.451, C:E.452, C:S.453, C:G.454, C:R.455, C:S.456, C:T.541

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: F.263, E.291, D.315 Ligands: OXL.3 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.5: 5 residues within 4Å: Chain B: N.94, S.96, D.132, T.133, S.262 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.96, B:D.132, B:T.133 MG.9: 4 residues within 4Å: Chain C: F.263, E.291, D.315 Ligands: OXL.10 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.291, C:D.315, H2O.3, H2O.4 MG.12: 5 residues within 4Å: Chain D: N.94, S.96, D.132, T.133, S.262 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:S.96, D:D.132, D:T.133

2 x OXL: OXALATE ION(Non-covalent)

OXL.3: 9 residues within 4Å: Chain A: R.92, K.289, E.291, A.312, R.313, G.314, D.315, T.347 Ligands: MG.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.314, A:D.315, A:T.347, A:T.347, A:T.347 Water bridges: A:S.262 Salt bridges: A:R.92, A:K.289 OXL.10: 9 residues within 4Å: Chain C: R.92, K.289, E.291, A.312, R.313, G.314, D.315, T.347 Ligands: MG.9 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.314, C:D.315, C:T.347, C:T.347 Water bridges: C:S.262 Salt bridges: C:R.92, C:K.289

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: R.62, N.63, T.64, G.65, N.89, H.483, Y.485, I.488, F.489 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.89, A:H.483, A:H.483 GOL.6: 5 residues within 4Å: Chain B: D.388, Y.389, P.390, L.391, E.392 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.391, B:E.392, B:E.392 GOL.7: 9 residues within 4Å: Chain B: R.62, N.63, T.64, G.65, N.89, H.483, I.488, F.489, P.490 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.62, B:N.89, B:H.483, B:H.483 GOL.11: 9 residues within 4Å: Chain C: R.62, N.63, T.64, G.65, N.89, H.483, Y.485, I.488, F.489 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.89, C:H.483 GOL.13: 5 residues within 4Å: Chain D: D.388, Y.389, P.390, L.391, E.392 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.391, D:E.392, D:E.392 GOL.14: 9 residues within 4Å: Chain D: R.62, N.63, T.64, G.65, N.89, H.483, I.488, F.489, P.490 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.62, D:N.89, D:H.483

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

2020-10-07

Peptides

Pyruvate kinase PKM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
C

D
A

Pyruvate kinase PKM