SMTL ID : 3bjf.1

Pyruvate kinase M2 is a phosphotyrosine binding protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-tetramer

Ligands

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

FBP.1: 18 residues within 4Å: Chain A: L.418, T.419, K.420, S.421, G.422, 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 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.419, A:T.419, A:K.420, A:S.421, A:G.422, A:S.424, A:S.424, A:S.424, A:G.501, A:R.503, A:G.505, A:G.507, A:F.508, A:F.508, A:T.509 Salt bridges: A:K.420, A:R.476 FBP.5: 16 residues within 4Å: Chain B: L.418, T.419, K.420, S.421, R.423, S.424, W.469, R.476, G.501, R.503, P.504, G.505, S.506, G.507, F.508, T.509 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:T.419, B:K.420, B:S.421, B:G.422, B:S.424, B:S.424, B:S.424, B:G.501, B:R.503, B:R.503, B:G.505, B:G.507, B:F.508 Water bridges: B:R.423, B:R.423, B:W.469, B:D.472, B:R.476, B:R.476, B:R.476, B:T.509, B:T.509 Salt bridges: B:K.420, B:R.476 FBP.9: 16 residues within 4Å: Chain C: L.418, T.419, K.420, S.421, R.423, S.424, W.469, R.476, G.501, R.503, P.504, G.505, S.506, G.507, F.508, T.509 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:T.419, C:T.419, C:K.420, C:S.421, C:G.422, C:S.424, C:S.424, C:S.424, C:G.501, C:R.503, C:G.505, C:G.507, C:F.508, C:F.508, C:T.509 Water bridges: C:R.423, C:R.423 Salt bridges: C:K.420, C:R.423, C:R.476 FBP.13: 17 residues within 4Å: Chain D: 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 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:T.419, D:K.420, D:S.421, D:S.424, D:S.424, D:G.501, D:R.503, D:G.505, D:G.507, D:F.508, D:F.508 Water bridges: D:L.418, D:T.509 Salt bridges: D:K.420, D:R.476

4 x OXL: OXALATE ION(Non-covalent)

OXL.2: 9 residues within 4Å: Chain A: K.257, E.259, M.278, A.280, R.281, G.282, D.283, T.315 Ligands: K.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.259, A:G.282, A:D.283, A:D.283, A:T.315 Water bridges: A:K.257 Salt bridges: A:R.60, A:K.257 OXL.6: 9 residues within 4Å: Chain B: K.257, E.259, M.278, A.280, R.281, G.282, D.283, T.315 Ligands: K.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.282, B:D.283, B:D.283, B:D.283, B:T.315, B:T.315 Water bridges: B:R.60 Salt bridges: B:R.60, B:K.257, B:K.257 OXL.10: 9 residues within 4Å: Chain C: K.257, E.259, M.278, A.280, R.281, G.282, D.283, T.315 Ligands: K.11 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.282, C:D.283, C:D.283, C:T.315 Water bridges: C:R.60 Salt bridges: C:R.60, C:K.257, C:K.257 OXL.14: 10 residues within 4Å: Chain D: K.257, E.259, M.278, A.280, R.281, G.282, D.283, T.315, M.347 Ligands: K.15 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:E.259, D:G.282, D:D.283, D:D.283, D:T.315, D:T.315 Water bridges: D:R.60 Salt bridges: D:R.60, D:K.257, D:K.257

4 x K: POTASSIUM ION(Non-covalent)

K.3: 2 residues within 4Å: Chain A: D.283 Ligands: OXL.2 No protein-ligand interaction detected (PLIP) K.7: 6 residues within 4Å: Chain B: S.230, F.231, K.257, E.259, D.283 Ligands: OXL.6 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.259, H2O.6 K.11: 6 residues within 4Å: Chain C: S.230, F.231, K.257, E.259, D.283 Ligands: OXL.10 No protein-ligand interaction detected (PLIP) K.15: 6 residues within 4Å: Chain D: S.230, F.231, K.257, E.259, D.283 Ligands: OXL.14 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.259, H2O.18, H2O.21

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: N.62, S.64, D.100, T.101, S.230, K.257 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.100, A:T.101, H2O.1 MG.8: 6 residues within 4Å: Chain B: N.62, S.64, D.100, T.101, S.230, K.257 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.64, B:D.100, B:T.101, H2O.6, H2O.10 MG.12: 6 residues within 4Å: Chain C: N.62, S.64, D.100, T.101, S.230, K.257 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.100, C:T.101, H2O.13 MG.16: 6 residues within 4Å: Chain D: N.62, S.64, D.100, T.101, S.230, K.257 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.100, D:T.101, H2O.18, H2O.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Christofk, H.R. et al., Pyruvate kinase M2 is a phosphotyrosine-binding protein. Nature (2008)

Release Date

2008-03-04

Peptides

Pyruvate kinase isozymes M1/M2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase isozymes M1/M2