SMTL ID : 6nu1.5 (4 other biounits)

Crystal Structure of Human PKM2 in Complex with L-cysteine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

2 x CYS: CYSTEINE(Non-covalent)

CYS.1: 9 residues within 4Å: Chain A: R.63, N.64, N.90, R.126, H.484, G.488, I.489, F.490, P.491 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:N.90, A:H.484, A:I.489, C.1 Water bridges: A:H.484, A:I.489 Salt bridges: A:R.63, A:R.126, A:H.484 CYS.6: 10 residues within 4Å: Chain B: R.63, N.64, T.65, N.90, R.126, H.484, G.488, I.489, F.490, P.491 9 PLIP interactions: 1 Ligand-Ligand interactions, 8 interactions with chain B Hydrogen bonds: C.6, B:N.90, B:H.484, B:H.484, B:I.489 Water bridges: B:R.126 Salt bridges: B:R.63, B:R.126, B:H.484

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

FBP.2: 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 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.452, A:K.453, A:S.454, A:G.455, A:R.456, A:S.457, A:S.457, A:G.534, A:R.536, A:G.538, A:G.540, A:F.541, A:F.541 Salt bridges: A:K.453, A:R.509 FBP.7: 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 15 PLIP interactions: 15 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:R.536, B:G.538, B:G.540, B:F.541 Water bridges: B:R.509, B:T.542 Salt bridges: B:R.509

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.292, D.316 Ligands: OXL.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.292, A:D.316, H2O.2, H2O.3 MG.8: 3 residues within 4Å: Chain B: E.292, D.316 Ligands: OXL.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.292, B:D.316, H2O.10, H2O.10

2 x OXL: OXALATE ION(Non-covalent)

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

1 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Srivastava, D. et al., Mechanistic and Structural Insights into Cysteine-Mediated Inhibition of Pyruvate Kinase Muscle Isoform 2. Biochemistry (2019)

Release Date

2019-08-21

Peptides

Pyruvate kinase PKM: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

Pyruvate kinase PKM

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