SMTL ID : 4yj5.1

Crystal structure of PKM2 mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-tetramer

Ligands

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.1: 7 residues within 4Å: Chain A: K.257, E.259, A.280, R.281, G.282, D.283, T.315 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.257, A:E.259, A:G.282, A:D.283, A:T.315, A:T.315 Water bridges: A:R.60 PYR.4: 8 residues within 4Å: Chain B: R.60, K.257, E.259, A.280, R.281, G.282, D.283, T.315 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.257, B:G.282, B:D.283, B:D.283, B:T.315, B:T.315 PYR.8: 7 residues within 4Å: Chain C: K.257, E.259, A.280, R.281, G.282, D.283, T.315 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.257, C:E.259, C:G.282, C:D.283, C:D.283, C:D.283 PYR.12: 9 residues within 4Å: Chain D: R.60, D.165, K.257, E.259, A.280, R.281, G.282, D.283, T.315 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.257, D:E.259, D:G.282, D:D.283, D:D.283

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: N.62, S.64, D.100, T.101, S.230, K.257 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.64, A:D.100, A:T.101, H2O.2, H2O.3 MG.5: 6 residues within 4Å: Chain B: N.62, S.64, D.100, T.101, S.230, K.257 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.64, B:D.100, B:T.101, H2O.6 MG.9: 6 residues within 4Å: Chain C: N.62, S.64, D.100, T.101, S.230, K.257 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.64, C:D.100, C:T.101 MG.13: 6 residues within 4Å: Chain D: N.62, S.64, D.100, T.101, E.105, S.230 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.100, D:T.101

4 x SER: SERINE(Non-covalent)

SER.3: 8 residues within 4Å: Chain A: R.30, N.31, N.57, R.93, H.451, I.456, F.457, P.458 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.30, A:N.57, A:H.451 Water bridges: A:R.30, A:N.31, A:R.93, A:R.93, A:H.451 Salt bridges: A:R.30, A:R.93, A:H.451 SER.6: 8 residues within 4Å: Chain B: R.30, N.31, N.57, R.93, H.451, I.456, F.457, P.458 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.30, B:N.57, B:N.57, B:H.451 Water bridges: B:R.30, B:R.30, B:N.31, B:H.451 Salt bridges: B:R.30, B:R.93, B:H.451 SER.10: 8 residues within 4Å: Chain C: R.30, N.31, N.57, R.93, H.451, I.456, F.457, P.458 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:R.30, C:N.57, C:H.451 Water bridges: C:R.30, C:R.30, C:R.93, C:R.93 Salt bridges: C:R.30, C:R.93, C:H.451 SER.14: 7 residues within 4Å: Chain D: R.30, N.31, N.57, H.451, I.456, F.457, P.458 7 PLIP interactions: 6 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: D:R.30, D:N.57, D:N.57, D:H.451 Salt bridges: D:R.30, D:H.451 Water bridges: S.14

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

FBP.7: 17 residues within 4Å: Chain B: L.418, T.419, K.420, S.421, R.423, S.424, W.469, R.476, G.501, W.502, R.503, P.504, G.505, S.506, G.507, F.508, T.509 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:T.419, B:K.420, B:S.421, B:G.422, B:S.424, B:G.501, B:R.503, B:S.506, B:S.506, B:F.508 Water bridges: B:R.476, B:R.476 Salt bridges: B:K.420, B:R.476 FBP.11: 17 residues within 4Å: Chain C: L.418, T.419, K.420, S.421, G.422, R.423, S.424, W.469, R.476, G.501, R.503, P.504, G.505, S.506, G.507, F.508, T.509 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:T.419, C:K.420, C:S.421, C:G.422, C:S.424, C:S.424, C:G.501, C:S.506, C:S.506, C:F.508, C:T.509 Water bridges: C:R.423, C:T.509 Salt bridges: C:K.420, C:R.476 FBP.15: 18 residues within 4Å: Chain D: L.418, T.419, K.420, S.421, G.422, R.423, S.424, W.469, R.476, T.500, G.501, R.503, P.504, G.505, S.506, G.507, F.508, T.509 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:T.419, D:K.420, D:S.421, D:G.422, D:S.424, D:S.424, D:G.501, D:R.503, D:S.506, D:S.506, D:F.508, D:T.509 Water bridges: D:R.476, D:R.476, D:R.476 Salt bridges: D:K.420, D:R.476

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, T.J. et al., Mutations in the PKM2 exon-10 region are associated with reduced allostery and increased nuclear translocation. Commun Biol (2019)

Release Date

2016-03-09

Peptides

Pyruvate kinase PKM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase PKM