SMTL ID : 6nub.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x SER: SERINE(Non-covalent)

SER.1: 8 residues within 4Å: Chain A: R.62, N.63, N.89, R.125, H.483, I.488, F.489, P.490 13 PLIP interactions: 2 Ligand-Ligand interactions, 11 interactions with chain A Hydrogen bonds: S.1, S.1, A:R.62, A:N.89, A:H.483 Water bridges: A:R.62, A:R.62, A:N.63, A:R.125, A:I.488 Salt bridges: A:R.62, A:R.125, A:H.483 SER.9: 8 residues within 4Å: Chain B: R.62, N.63, N.89, R.125, H.483, I.488, F.489, P.490 11 PLIP interactions: 10 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:R.62, B:N.89, B:H.483, B:I.488, S.9 Water bridges: B:R.62, B:N.63, B:R.125 Salt bridges: B:R.62, B:R.125, B:H.483

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.291, D.315 Ligands: OXL.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.291, A:D.315, H2O.3, H2O.7 MG.10: 3 residues within 4Å: Chain B: E.291, D.315 Ligands: OXL.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.291, B:D.315, H2O.23, H2O.26

2 x OXL: OXALATE ION(Non-covalent)

OXL.3: 9 residues within 4Å: Chain A: R.92, K.289, E.291, A.312, R.313, G.314, D.315, T.347 Ligands: MG.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.314, A:D.315, A:D.315, A:T.347, A:T.347, A:T.347 Water bridges: A:R.92, A:R.92, A:R.92, A:K.289, A:K.289, A:S.381 Salt bridges: A:R.92, A:K.289, A:K.289 OXL.11: 9 residues within 4Å: Chain B: R.92, K.289, E.291, A.312, R.313, G.314, D.315, T.347 Ligands: MG.10 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:E.291, B:G.314, B:D.315, B:T.347, B:T.347, B:T.347 Water bridges: B:R.92 Salt bridges: B:R.92, B:K.289, B:K.289

2 x K: POTASSIUM ION(Non-covalent)

K.4: 6 residues within 4Å: Chain A: N.94, S.96, D.132, T.133, S.262, K.289 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.96, A:D.132, A:T.133, H2O.8, H2O.14 K.12: 5 residues within 4Å: Chain B: N.94, S.96, D.132, T.133, S.262 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.96, B:D.132, B:T.133, H2O.22, H2O.35

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

SCN.5: 3 residues within 4Å: Chain A: E.304, A.339, K.341 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.304 SCN.6: 6 residues within 4Å: Chain A: K.285, D.307, P.342, H.458, L.484, Y.485 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.485 Water bridges: A:H.458 SCN.13: 6 residues within 4Å: Chain B: K.285, D.307, P.342, H.458, L.484, Y.485 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.485 Water bridges: B:D.307 SCN.14: 7 residues within 4Å: Chain A: I.54, D.55 Chain B: H.293, E.319, I.320, P.321, K.324 No protein-ligand interaction detected (PLIP) SCN.15: 4 residues within 4Å: Chain B: V.270, H.271, R.274, A.305 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 4 residues within 4Å: Chain A: K.524, G.525, V.549, P.550 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.525, A:V.549 Water bridges: A:K.524, A:P.550

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

B3P.8: 7 residues within 4Å: Chain A: D.196, L.199, K.226, Q.348, E.351, S.381, G.382 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.226, A:Q.348, A:E.351, A:G.382 Water bridges: A:E.351, A:S.381 B3P.18: 9 residues within 4Å: Chain A: K.356 Chain B: D.196, D.197, L.199, K.226, Q.348, E.351, S.381, G.382 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.197, B:K.226, B:Q.348, B:E.351, B:G.382 Water bridges: B:D.196, B:E.351, B:S.381, A:K.356, A:K.356

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.16: 7 residues within 4Å: Chain A: F.45, L.372, Q.412 Chain B: F.45, L.372, D.373 Ligands: EDO.17 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.373 Water bridges: B:K.330, B:D.373, B:D.373, A:D.373

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

EDO.17: 7 residues within 4Å: Chain B: F.45, H.48, L.52, L.372, A.407, Y.409 Ligands: PG4.16 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.330

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