SMTL ID : 4fxf.1

Structure of M2 pyruvate kinase in complex with phenylalanine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-tetramer

Ligands

4 x OXL: OXALATE ION(Non-covalent)

OXL.1: 9 residues within 4Å: Chain A: K.290, E.292, M.311, A.313, R.314, G.315, D.316, T.348 Ligands: MG.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.292, A:G.315, A:D.316, A:T.348 Water bridges: A:K.290 Salt bridges: A:R.93, A:K.290 OXL.5: 10 residues within 4Å: Chain B: K.290, E.292, A.313, R.314, G.315, D.316, T.348, M.380 Ligands: MG.7, ATP.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.292, B:E.292, B:G.315, B:D.316, B:T.348 Water bridges: B:R.93 Salt bridges: B:R.93, B:K.290 OXL.11: 8 residues within 4Å: Chain C: K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.13 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:E.292, C:G.315, C:D.316, C:T.348, C:T.348 Water bridges: C:K.290 Salt bridges: C:R.93, C:K.290, C:K.290 OXL.15: 11 residues within 4Å: Chain D: R.93, K.290, E.292, M.311, A.313, R.314, G.315, D.316, T.348 Ligands: MG.17, ATP.18 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.315, D:D.316, D:D.316, D:D.316, D:T.348, D:T.348 Water bridges: D:S.263 Salt bridges: D:R.93, D:K.290

4 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: N.95, S.97, D.133, T.134, S.263, K.290 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.97, A:D.133, A:T.134, H2O.1 K.6: 7 residues within 4Å: Chain B: N.95, S.97, D.133, T.134, S.263, K.290 Ligands: ATP.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.97, B:D.133, B:T.134, H2O.6 K.12: 6 residues within 4Å: Chain C: N.95, S.97, D.133, T.134, S.263, K.290 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.97, C:D.133, C:T.134, H2O.11 K.16: 7 residues within 4Å: Chain D: N.95, S.97, D.133, T.134, S.263, K.290 Ligands: ATP.18 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.133, D:T.134

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.292, D.316 Ligands: OXL.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.292, A:D.316, H2O.1, H2O.3 MG.7: 4 residues within 4Å: Chain B: E.292, D.316 Ligands: OXL.5, ATP.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.292, B:D.316 MG.9: 4 residues within 4Å: Chain B: D.198, T.348, S.382 Ligands: ATP.8 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain C: E.292, D.316 Ligands: OXL.11 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.292, C:D.316, H2O.7, H2O.7 MG.17: 4 residues within 4Å: Chain D: E.292, D.316 Ligands: OXL.15, ATP.18 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.292, D:D.316, H2O.12 MG.19: 2 residues within 4Å: Chain D: S.382 Ligands: ATP.18 No protein-ligand interaction detected (PLIP)

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

FBP.4: 17 residues within 4Å: Chain A: L.451, T.452, K.453, S.454, R.456, S.457, W.502, R.509, G.534, W.535, R.536, P.537, G.538, S.539, G.540, F.541, T.542 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.452, A:K.453, A:S.454, A:G.455, A:S.457, A:S.457, A:G.534, A:G.538, A:S.539, A:G.540, A:F.541, A:T.542 Water bridges: A:R.456, A:T.542 Salt bridges: A:R.509 FBP.10: 17 residues within 4Å: Chain B: L.451, T.452, K.453, S.454, R.456, S.457, W.502, R.509, T.533, G.534, R.536, P.537, G.538, S.539, G.540, F.541, T.542 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.452, B:T.452, B:K.453, B:S.454, B:S.457, B:S.457, B:R.509, B:R.509, B:G.534, B:G.538, B:S.539, B:G.540, B:F.541, B:T.542 Salt bridges: B:R.509 FBP.14: 16 residues within 4Å: Chain C: 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 C Hydrogen bonds: C:T.452, C:K.453, C:S.454, C:S.457, C:G.534, C:R.536, C:G.538, C:S.539, C:G.540, C:F.541 Water bridges: C:R.456 Salt bridges: C:K.453, C:R.456, C:R.509 FBP.20: 18 residues within 4Å: Chain D: L.451, T.452, K.453, S.454, G.455, R.456, S.457, W.502, R.509, G.534, W.535, R.536, P.537, G.538, S.539, G.540, F.541, T.542 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:T.452, D:K.453, D:S.454, D:G.455, D:S.457, D:S.457, D:S.457, D:G.534, D:R.536, D:G.538, D:G.540, D:F.541 Water bridges: D:S.454, D:S.454, D:R.456, D:R.509 Salt bridges: D:K.453, D:R.509

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.8: 21 residues within 4Å: Chain B: T.70, P.73, R.93, N.95, H.98, Y.103, H.104, D.133, R.140, D.198, K.227, K.290, D.316, S.382, G.383, A.386, K.387 Ligands: OXL.5, K.6, MG.7, MG.9 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:N.95, B:S.97, B:Y.103, B:K.227, B:K.227, B:S.382 Water bridges: B:I.71, B:I.71, B:R.93, B:R.93, B:H.104, B:R.140, B:R.140, B:D.197, B:D.198, B:S.263, B:T.348 Salt bridges: B:R.93, B:R.93, B:H.98, B:R.140, B:R.140, B:K.290 pi-Stacking: B:H.98, B:H.98 ATP.18: 21 residues within 4Å: Chain D: T.70, I.71, P.73, R.93, N.95, H.98, Y.103, H.104, R.140, D.198, K.227, K.290, D.316, S.382, G.383, A.386, K.387 Ligands: OXL.15, K.16, MG.17, MG.19 22 PLIP interactions: 22 interactions with chain D Hydrogen bonds: D:I.71, D:N.95, D:K.227, D:K.227 Water bridges: D:H.104, D:R.140, D:R.140, D:K.290, D:K.290, D:T.348, D:T.348, D:S.382, D:S.382, D:S.382, D:G.383 Salt bridges: D:R.93, D:R.93, D:H.98, D:R.140, D:R.140, D:K.290 pi-Stacking: D:H.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morgan, H.P. et al., M2 pyruvate kinase provides a mechanism for nutrient sensing and regulation of cell proliferation. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-03-27

Peptides

Pyruvate kinase isozymes M1/M2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
C

D
B

Pyruvate kinase isozymes M1/M2

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