SMTL ID : 4qg8.1

crystal structure of PKM2-K305Q mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.276, D.300 Ligands: MLI.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.300, H2O.7 MG.5: 3 residues within 4Å: Chain B: E.276, D.300 Ligands: MLI.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.276, B:D.300, H2O.12 MG.8: 3 residues within 4Å: Chain C: E.276, D.300 Ligands: MLI.10 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.276, C:D.300, H2O.21

3 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: N.79, S.81, D.117, T.118, S.247, K.274 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.81, A:D.117, A:T.118, H2O.2, H2O.5 K.6: 7 residues within 4Å: Chain B: N.79, S.81, D.117, T.118, E.122, S.247, K.274 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.81, B:D.117, B:T.118, H2O.8, H2O.8 K.9: 7 residues within 4Å: Chain C: N.79, S.81, D.117, T.118, E.122, S.247, K.274 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.81, C:D.117, C:T.118, H2O.16, H2O.20

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: R.47, N.48, G.50, N.74, H.468, Y.470, I.473, F.474, P.475 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.47, A:N.74, A:Y.470

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

MLI.4: 8 residues within 4Å: Chain A: K.274, E.276, A.297, R.298, G.299, D.300, T.332 Ligands: MG.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.297 Hydrogen bonds: A:E.276, A:E.276, A:G.299, A:D.300 Water bridges: A:N.79, A:K.274 Salt bridges: A:R.77, A:K.274 MLI.7: 8 residues within 4Å: Chain B: K.274, E.276, A.297, R.298, G.299, D.300, T.332 Ligands: MG.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.297 Hydrogen bonds: B:G.299, B:D.300, B:D.300, B:T.332 Water bridges: B:R.77, B:K.274, B:K.274, B:E.276 Salt bridges: B:R.77, B:K.274 MLI.10: 8 residues within 4Å: Chain C: K.274, E.276, A.297, R.298, G.299, D.300, T.332 Ligands: MG.8 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:A.297 Hydrogen bonds: C:G.299, C:D.300, C:T.332, C:T.332 Water bridges: C:K.274, C:K.274, C:K.274 Salt bridges: C:R.77, C:K.274

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, P. et al., Structural insight into mechanisms for dynamic regulation of PKM2. Protein Cell (2015)

Release Date

2015-02-25

Peptides

Pyruvate kinase PKM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase PKM