SMTL ID : 6b6u.1

Pyruvate Kinase M2 mutant - S437Y

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: F.238, K.264, E.266, A.287, D.290 Ligands: OXL.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.266, A:D.290, H2O.4, H2O.9 MG.10: 5 residues within 4Å: Chain B: K.264, E.266, A.287, D.290 Ligands: OXL.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.266, B:D.290, H2O.23, H2O.27

2 x OXL: OXALATE ION(Non-covalent)

OXL.2: 10 residues within 4Å: Chain A: R.67, K.264, E.266, A.287, R.288, G.289, D.290, T.322, M.354 Ligands: MG.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.289, A:D.290, A:D.290, A:T.322, A:T.322, A:T.322 Water bridges: A:R.67, A:K.264, A:K.264 Salt bridges: A:R.67, A:K.264, A:K.264 OXL.11: 10 residues within 4Å: Chain B: R.67, K.264, E.266, A.287, R.288, G.289, D.290, T.322, M.354 Ligands: MG.10 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.289, B:D.290, B:T.322, B:T.322, B:T.322 Water bridges: B:R.67, B:K.264 Salt bridges: B:R.67, B:K.264, B:K.264

2 x K: POTASSIUM ION(Non-covalent)

K.3: 8 residues within 4Å: Chain A: R.67, N.69, S.71, D.107, T.108, K.109, S.237, K.264 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.71, A:D.107, A:T.108, H2O.7, H2O.14 K.12: 8 residues within 4Å: Chain B: R.67, N.69, S.71, D.107, T.108, K.109, S.237, K.264 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.71, B:D.107, B:T.108, H2O.27, H2O.35

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 7 residues within 4Å: Chain A: N.38, G.40, H.458, Y.460, R.461, G.462, I.463 Ligand excluded by PLIP CL.13: 7 residues within 4Å: Chain B: N.38, G.40, H.458, Y.460, R.461, G.462, I.463 Ligand excluded by PLIP

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

SCN.5: 6 residues within 4Å: Chain A: H.268, I.295, P.296, K.299 Chain B: I.29, D.30 No protein-ligand interaction detected (PLIP) SCN.6: 4 residues within 4Å: Chain A: L.278, E.279, A.314, K.316 No protein-ligand interaction detected (PLIP) SCN.7: 7 residues within 4Å: Chain A: K.260, I.262, D.282, P.317, H.433, L.459, Y.460 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.260, A:Y.460 SCN.14: 7 residues within 4Å: Chain B: K.260, I.262, D.282, P.317, H.433, L.459, Y.460 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.260, B:Y.460 Water bridges: B:D.282, B:D.282 SCN.15: 7 residues within 4Å: Chain A: I.29, D.30 Chain B: H.268, E.294, I.295, P.296, K.299 No protein-ligand interaction detected (PLIP) SCN.16: 4 residues within 4Å: Chain B: V.245, H.246, R.249, A.280 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.249

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

PEG.8: 5 residues within 4Å: Chain A: K.499, G.500, P.523, V.524, P.525 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.524, A:P.525 Water bridges: A:G.500

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

B3P.9: 12 residues within 4Å: Chain A: D.171, D.172, L.174, K.201, T.322, Q.323, E.326, I.329, S.356, G.357, E.358 Chain B: K.331 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.201, A:Q.323, A:E.326, A:G.357, A:E.358 Water bridges: A:D.172, A:D.172, A:D.172, A:Q.323, A:S.356 B3P.19: 12 residues within 4Å: Chain A: K.331 Chain B: D.171, D.172, L.174, K.201, T.322, Q.323, E.326, I.329, S.356, G.357, E.358 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.171, B:D.172, B:K.201, B:Q.323, B:E.326, B:G.357 Water bridges: B:D.171, B:S.356, A:K.331, A:K.331

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

PG4.17: 13 residues within 4Å: Chain A: F.20, M.24, K.305, L.347, D.348, Y.384, Q.387, L.388 Chain B: F.20, K.305, L.347, D.348 Ligands: EDO.18 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Water bridges: A:K.305, A:D.348, B:K.305, B:K.305, B:D.348, B:D.348 Hydrogen bonds: B:D.348

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

EDO.18: 10 residues within 4Å: Chain A: K.305 Chain B: F.20, H.23, M.24, L.27, L.347, A.382, I.383, Y.384 Ligands: PG4.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Srivastava, D. et al., Structural Investigation of a Dimeric Variant of Pyruvate Kinase Muscle Isoform 2. Biochemistry (2017)

Release Date

2017-12-20

Peptides

Pyruvate kinase PKM: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyruvate kinase PKM