SMTL ID : 6nu5.1

Pyruvate Kinase M2 Mutant - S437Y in Complex with L-cysteine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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 10 PLIP interactions: 9 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:N.90, A:H.484, A:I.489, C.1 Water bridges: A:R.63, A:N.64, A:R.126 Salt bridges: A:R.63, A:R.126, A:H.484 CYS.7: 9 residues within 4Å: Chain B: R.63, N.64, N.90, R.126, H.484, G.488, I.489, F.490, P.491 10 PLIP interactions: 9 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:N.90, B:H.484, B:I.489, C.7 Water bridges: B:N.64, B:R.126, B:H.484 Salt bridges: B:R.63, B:R.126, B:H.484

2 x OXL: OXALATE ION(Non-covalent)

OXL.2: 9 residues within 4Å: Chain A: R.93, K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.315, A:D.316, A:D.316, A:T.348, A:T.348, A:T.348 Water bridges: A:R.93, A:K.290 Salt bridges: A:R.93, A:K.290, A:K.290 OXL.8: 9 residues within 4Å: Chain B: R.93, K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.13 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.315, B:D.316, B:T.348, B:T.348, B:T.348 Water bridges: B:R.93, B:K.290 Salt bridges: B:R.93, B:K.290, B:K.290

2 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.3: 6 residues within 4Å: Chain A: K.286, D.308, P.343, H.459, L.485, Y.486 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.486 SCN.9: 6 residues within 4Å: Chain B: K.286, D.308, P.343, H.459, L.485, Y.486 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.486 Water bridges: B:D.308

2 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.4: 8 residues within 4Å: Chain A: D.197, L.200, K.227, Q.349, E.352, S.382, G.383 Chain B: K.357 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.227, A:Q.349, A:E.352, A:G.383, A:E.384 Water bridges: A:H.98, A:G.224, A:S.382 B3P.10: 9 residues within 4Å: Chain A: K.357 Chain B: D.197, D.198, L.200, K.227, Q.349, E.352, S.382, G.383 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.198, B:K.227, B:Q.349, B:E.352, B:G.383 Water bridges: B:H.98, B:D.197, B:E.352, B:S.382, A:K.357, A:K.357, A:K.357

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: E.292, D.316 Ligands: OXL.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.292, A:D.316, H2O.4, H2O.6 MG.13: 3 residues within 4Å: Chain B: E.292, D.316 Ligands: OXL.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.292, B:D.316, H2O.24, H2O.26

2 x K: POTASSIUM ION(Non-covalent)

K.6: 6 residues within 4Å: Chain A: N.95, S.97, D.133, T.134, S.263, K.290 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.97, A:D.133, A:T.134, H2O.8, H2O.14 K.14: 5 residues within 4Å: Chain B: N.95, S.97, D.133, T.134, S.263 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.97, B:D.133, B:T.134, H2O.22, H2O.33

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 4 residues within 4Å: Chain B: V.271, H.272, R.275, A.306 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.271, B:R.275 EDO.12: 5 residues within 4Å: Chain B: F.46, H.49, L.53, L.373, A.408 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.331

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
A

B
B

Pyruvate kinase PKM