SMTL ID : 4b2d.1

human PKM2 with L-serine and FBP bound.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-3-1-mer

Ligands

4 x SER: SERINE(Non-covalent)

SER.1: 11 residues within 4Å: Chain A: R.60, N.61, T.62, G.63, N.87, R.123, H.481, G.485, I.486, F.487, P.488 9 PLIP interactions: 2 Ligand-Ligand interactions, 7 interactions with chain A Hydrogen bonds: S.1, S.1, A:N.87, A:N.87, A:H.481, A:G.485 Salt bridges: A:R.60, A:R.123, A:H.481 SER.4: 9 residues within 4Å: Chain B: R.60, N.61, T.62, N.87, R.123, H.481, I.486, F.487, P.488 12 PLIP interactions: 9 interactions with chain B, 3 Ligand-Ligand interactions Hydrogen bonds: B:N.87, B:N.87, B:H.481, B:I.486, S.4, S.4, S.4 Water bridges: B:R.60, B:R.123 Salt bridges: B:R.60, B:R.123, B:H.481 SER.6: 10 residues within 4Å: Chain C: R.60, N.61, T.62, N.87, R.123, H.481, G.485, I.486, F.487, P.488 13 PLIP interactions: 12 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:N.87, C:N.87, C:H.481, C:I.486, C:I.486, S.6 Water bridges: C:R.60, C:R.60, C:R.123, C:R.123 Salt bridges: C:R.60, C:R.123, C:H.481 SER.9: 10 residues within 4Å: Chain D: R.60, N.61, T.62, G.63, N.87, R.123, H.481, I.486, F.487, P.488 10 PLIP interactions: 2 Ligand-Ligand interactions, 8 interactions with chain D Hydrogen bonds: S.9, S.9, D:R.60, D:N.87, D:I.486, D:I.486 Water bridges: D:R.123 Salt bridges: D:R.60, D:R.123, D:H.481

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

FBP.2: 16 residues within 4Å: Chain A: L.448, T.449, K.450, S.451, R.453, S.454, W.499, R.506, G.531, R.533, P.534, G.535, S.536, G.537, F.538, T.539 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:T.449, A:K.450, A:S.451, A:S.454, A:S.454, A:G.531, A:R.533, A:R.533, A:G.535, A:G.537, A:F.538 Water bridges: A:L.448, A:K.450, A:K.450, A:R.453, A:R.506, A:R.506 Salt bridges: A:K.450, A:R.506 FBP.5: 16 residues within 4Å: Chain B: L.448, T.449, K.450, S.451, R.453, S.454, W.499, R.506, G.531, R.533, P.534, G.535, S.536, G.537, F.538, T.539 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:K.450, B:S.451, B:G.452, B:S.454, B:S.454, B:S.454, B:G.531, B:R.533, B:R.533, B:G.535, B:S.536, B:G.537, B:F.538, B:T.539 Water bridges: B:R.453, B:R.453, B:D.502, B:R.506, B:R.506, B:R.506, B:T.539 Salt bridges: B:K.450, B:R.506 FBP.7: 16 residues within 4Å: Chain C: L.448, T.449, K.450, S.451, R.453, S.454, W.499, R.506, G.531, R.533, P.534, G.535, S.536, G.537, F.538, T.539 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:T.449, C:T.449, C:K.450, C:S.451, C:G.452, C:S.454, C:G.531, C:R.533, C:R.533, C:G.535, C:S.536, C:S.536, C:G.537, C:F.538, C:T.539 Water bridges: C:K.450, C:R.506, C:R.506, C:T.539 Salt bridges: C:K.450, C:R.453, C:R.506 FBP.10: 16 residues within 4Å: Chain D: L.448, T.449, K.450, S.451, R.453, S.454, W.499, R.506, G.531, R.533, P.534, G.535, S.536, G.537, F.538, T.539 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:T.449, D:K.450, D:S.451, D:G.452, D:S.454, D:S.454, D:S.454, D:G.531, D:R.533, D:R.533, D:G.535, D:S.536, D:G.537, D:F.538 Water bridges: D:R.506, D:R.506, D:R.506 Salt bridges: D:K.450, D:R.506

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: K.287, E.289, D.313 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.289, A:D.313, H2O.10 MG.8: 4 residues within 4Å: Chain C: F.261, K.287, E.289, D.313 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.289, C:D.313, H2O.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaneton, B. et al., Serine is a natural ligand and allosteric activator of pyruvate kinase M2. Nature (2012)

Release Date

2012-10-10

Peptides

PYRUVATE KINASE ISOZYMES M1/M2: ABC
PYRUVATE KINASE ISOZYMES M1/M2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PYRUVATE KINASE ISOZYMES M1/M2

PYRUVATE KINASE ISOZYMES M1/M2

Related Entries With Identical Sequence