SMTL ID : 5x0i.1

Crystal structure of PKM2 R399E mutant complexed with FBP and serine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 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.451, T.452, K.453, S.454, R.456, S.457, W.502, R.509, G.534, R.536, P.537, G.538, S.539, G.540, F.541, T.542 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.452, A:K.453, A:S.454, A:S.457, A:S.457, A:S.457, A:G.534, A:R.536, A:G.538, A:G.540, A:F.541 Salt bridges: A:K.453, A:R.509 FBP.6: 17 residues within 4Å: Chain B: L.451, T.452, K.453, S.454, G.455, R.456, S.457, W.502, R.509, G.534, R.536, P.537, G.538, S.539, G.540, F.541, T.542 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:T.452, B:T.452, B:K.453, B:S.454, B:G.455, B:S.457, B:S.457, B:G.534, B:G.538, B:G.540, B:F.541 Salt bridges: B:K.453, B:R.509 FBP.11: 17 residues within 4Å: Chain C: L.451, T.452, K.453, S.454, G.455, R.456, S.457, W.502, R.509, G.534, R.536, P.537, G.538, S.539, G.540, F.541, T.542 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:T.452, C:K.453, C:S.454, C:G.455, C:S.457, C:S.457, C:G.534, C:R.536, C:G.538, C:G.540, C:F.541, C:T.542 Salt bridges: C:K.453, C:R.509 FBP.16: 16 residues within 4Å: Chain D: L.451, T.452, K.453, S.454, R.456, S.457, W.502, R.509, G.534, R.536, P.537, G.538, S.539, G.540, F.541, T.542 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:T.452, D:T.452, D:K.453, D:S.454, D:S.457, D:S.457, D:G.534, D:G.538, D:G.540, D:F.541, D:T.542 Water bridges: D:L.451 Salt bridges: D:K.453, D:R.509

4 x SER: SERINE(Non-covalent)

SER.2: 8 residues within 4Å: Chain A: R.63, N.64, N.90, R.126, H.484, I.489, F.490, P.491 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.63, A:N.90, A:H.484 Salt bridges: A:R.63, A:R.126, A:H.484 SER.7: 8 residues within 4Å: Chain B: R.63, N.64, N.90, R.126, H.484, I.489, F.490, P.491 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.63, B:N.90, B:H.484 Salt bridges: B:R.63, B:R.126, B:H.484 SER.12: 8 residues within 4Å: Chain C: R.63, N.64, N.90, R.126, H.484, I.489, F.490, P.491 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.63, C:N.90, C:H.484 Salt bridges: C:R.126, C:H.484 SER.17: 9 residues within 4Å: Chain D: R.63, N.64, N.90, R.126, H.484, G.488, I.489, F.490, P.491 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.63, D:N.90, D:H.484 Salt bridges: D:R.126, D:H.484

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.3: 8 residues within 4Å: Chain A: K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.290, A:G.315, A:D.316, A:D.316, A:T.348 PYR.8: 8 residues within 4Å: Chain B: K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.290, B:G.315, B:D.316, B:T.348 PYR.13: 8 residues within 4Å: Chain C: K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.14 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.290, C:G.315, C:D.316, C:T.348, C:T.348 PYR.18: 9 residues within 4Å: Chain D: R.93, K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.19 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.290, D:G.315, D:D.316, D:T.348 Salt bridges: D:K.290

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: E.292, D.316 Ligands: PYR.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.292, A:D.316 MG.9: 4 residues within 4Å: Chain B: K.290, E.292, D.316 Ligands: PYR.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.292, B:D.316 MG.14: 4 residues within 4Å: Chain C: K.290, E.292, D.316 Ligands: PYR.13 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:E.292, C:D.316, PYR.13 MG.19: 5 residues within 4Å: Chain D: F.264, K.290, E.292, D.316 Ligands: PYR.18 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.292, D:D.316

4 x K: POTASSIUM ION(Non-covalent)

K.5: 6 residues within 4Å: Chain A: N.95, S.97, D.133, T.134, S.263, K.290 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.97, A:D.133, A:T.134 K.10: 6 residues within 4Å: Chain B: N.95, S.97, D.133, T.134, S.263, K.290 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.97, B:D.133, B:T.134, H2O.1 K.15: 6 residues within 4Å: Chain C: N.95, S.97, D.133, T.134, S.263, K.290 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.97, C:D.133, C:T.134 K.20: 6 residues within 4Å: Chain D: N.95, S.97, D.133, T.134, E.138, S.263 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:S.97, D:D.133, D:T.134

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

2018-01-31

Peptides

Pyruvate kinase PKM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase PKM