SMTL ID : 6wp4.1

Pyruvate Kinase M2 mutant-S37E

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

11 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 7 residues within 4Å: Chain A: T.451, K.452, S.453, R.455, S.456, S.538, G.539 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.451, A:T.451, A:K.452, A:S.453, A:R.455, A:S.456, A:S.456, A:G.539 Water bridges: A:R.455, A:R.455 PO4.2: 3 residues within 4Å: Chain A: H.97, G.98, T.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.98 PO4.3: 3 residues within 4Å: Chain A: H.293, E.294, R.297 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.293 Water bridges: A:H.293 Salt bridges: A:H.293, A:R.297 PO4.13: 7 residues within 4Å: Chain B: T.451, K.452, S.453, R.455, S.456, S.538, G.539 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.451, B:T.451, B:K.452, B:S.453, B:G.454, B:S.456, B:S.456, B:G.539 PO4.14: 3 residues within 4Å: Chain B: H.97, G.98, K.225 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.98 Salt bridges: B:H.97 PO4.24: 3 residues within 4Å: Chain C: H.97, G.98, T.99 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.98 PO4.25: 8 residues within 4Å: Chain C: T.451, K.452, S.453, R.455, S.456, G.537, S.538, G.539 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:T.451, C:K.452, C:S.453, C:S.456, C:S.456, C:S.456, C:S.456, C:S.538, C:G.539 PO4.26: 3 residues within 4Å: Chain C: H.293, E.294, R.297 3 PLIP interactions: 3 interactions with chain C Water bridges: C:E.294 Salt bridges: C:H.293, C:R.297 PO4.32: 8 residues within 4Å: Chain D: T.451, K.452, S.453, R.455, S.456, G.537, S.538, G.539 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:T.451, D:K.452, D:S.453, D:S.456, D:S.456, D:S.456, D:S.456, D:S.538, D:G.539 Water bridges: D:T.541 PO4.33: 2 residues within 4Å: Chain D: H.97, R.139 4 PLIP interactions: 4 interactions with chain D Water bridges: D:D.197, D:G.227 Salt bridges: D:H.97, D:R.139 PO4.34: 3 residues within 4Å: Chain D: S.96, H.97, G.98 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.98 Salt bridges: D:H.97

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: E.291, D.315 Ligands: OXL.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.291, A:D.315, H2O.4, H2O.4 MG.15: 3 residues within 4Å: Chain B: K.289, E.291, D.315 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.291, H2O.12 MG.27: 2 residues within 4Å: Chain C: E.291, D.315 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.291, C:D.315, H2O.13, H2O.14 MG.35: 3 residues within 4Å: Chain D: E.291, D.315 Ligands: OXL.38 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.291, D:D.315, H2O.19, H2O.20

5 x K: POTASSIUM ION(Non-covalent)

K.5: 6 residues within 4Å: Chain A: N.94, S.96, D.132, T.133, S.262, K.289 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.96, A:D.132, A:T.133, H2O.4 K.16: 6 residues within 4Å: Chain B: N.94, S.96, D.132, T.133, S.262, K.289 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.96, B:D.132, B:T.133, H2O.9, H2O.12 K.28: 5 residues within 4Å: Chain C: N.94, S.96, D.132, T.133, S.262 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.96, C:D.132, C:T.133, H2O.15, H2O.17 K.36: 6 residues within 4Å: Chain D: N.94, S.96, D.132, T.133, S.262, K.289 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.96, D:D.132, D:T.133, H2O.19 K.37: 2 residues within 4Å: Chain D: D.255, R.480 No protein-ligand interaction detected (PLIP)

2 x OXL: OXALATE ION(Non-covalent)

OXL.6: 9 residues within 4Å: Chain A: K.289, E.291, M.310, A.312, R.313, G.314, D.315, T.347 Ligands: MG.4 10 PLIP interactions: 10 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:K.289 Salt bridges: A:R.92, A:K.289, A:K.289 OXL.38: 9 residues within 4Å: Chain D: R.92, K.289, E.291, A.312, R.313, G.314, D.315, T.347 Ligands: MG.35 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.291, D:G.314, D:D.315, D:D.315 Salt bridges: D:R.92, D:K.289, D:K.289

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: H.100, Q.246, K.249, F.250 Ligand excluded by PLIP GOL.8: 3 residues within 4Å: Chain A: I.107, K.108, R.111 Ligand excluded by PLIP GOL.9: 3 residues within 4Å: Chain A: G.145, G.147, A.149 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: R.62, N.63, G.65, N.89, H.483, I.488, F.489 Ligand excluded by PLIP GOL.11: 8 residues within 4Å: Chain A: P.136, V.228, N.229, L.230, V.235, R.265, E.319 Ligands: GOL.12 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain A: E.137, I.138, G.227, V.228, F.263, D.315 Ligands: GOL.11 Ligand excluded by PLIP GOL.17: 9 residues within 4Å: Chain B: R.62, N.63, G.65, N.89, H.483, Y.485, G.487, I.488, F.489 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain B: N.94, S.96, H.97, E.137, R.139 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain B: P.136, V.228, N.229, L.230, V.235, E.319 Ligands: GOL.20 Ligand excluded by PLIP GOL.20: 8 residues within 4Å: Chain B: E.137, I.138, R.139, G.227, V.228, F.263, D.315 Ligands: GOL.19 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain B: H.410, L.411, F.414, F.440 Ligands: GOL.31 Ligand excluded by PLIP GOL.29: 8 residues within 4Å: Chain C: R.62, N.63, T.64, G.65, N.89, H.483, G.487, I.488 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain C: P.136, V.228, N.229, L.230, V.235, E.319 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain B: E.437, F.440, K.441 Chain C: R.418, V.433 Ligands: GOL.21 Ligand excluded by PLIP GOL.39: 6 residues within 4Å: Chain D: R.62, G.65, N.89, H.483, I.488, F.489 Ligand excluded by PLIP GOL.40: 6 residues within 4Å: Chain D: T.69, R.92, N.94, S.381, G.382, A.385 Ligand excluded by PLIP GOL.41: 7 residues within 4Å: Chain D: P.136, V.228, N.229, L.230, V.235, R.265, E.319 Ligand excluded by PLIP GOL.42: 3 residues within 4Å: Chain D: G.232, H.293, E.294 Ligand excluded by PLIP

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

CL.22: 2 residues within 4Å: Chain B: K.266, R.298 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain B: H.293, R.297 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nandi, S. et al., Structural basis for allosteric regulation of pyruvate kinase M2 by phosphorylation and acetylation. J.Biol.Chem. (2020)

Release Date

2020-09-30

Peptides

Pyruvate kinase PKM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
D

Pyruvate kinase PKM