SMTL ID : 6wp3.1

Pyruvate Kinase M2 Mutant-K433Q

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-tetramer

Ligands

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: R.62, N.63, G.65, N.89, H.483, Y.485, I.488, F.489, P.490 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.483, A:H.483 GOL.2: 7 residues within 4Å: Chain A: P.136, V.228, N.229, L.230, V.235, E.319 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.136, A:L.230 GOL.3: 8 residues within 4Å: Chain A: E.137, I.138, R.139, G.227, V.228, F.263, D.315 Ligands: GOL.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.137, A:I.138, A:I.138, A:V.228 Water bridges: A:S.96, A:S.96 GOL.4: 7 residues within 4Å: Chain A: I.70, G.71, R.75, L.93, Y.102, H.103, T.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.94, A:H.103, A:T.106 GOL.8: 10 residues within 4Å: Chain B: R.62, N.63, T.64, G.65, N.89, H.483, Y.485, I.488, F.489, P.490 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.483, B:H.483, B:I.488 GOL.9: 9 residues within 4Å: Chain B: P.136, I.138, V.228, N.229, L.230, V.235, F.263, R.265, E.319 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:P.136, B:L.230, B:R.265, B:E.319 Water bridges: B:I.138 GOL.10: 6 residues within 4Å: Chain B: T.451, Q.452, S.453, R.455, S.456, G.539 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.452, B:S.453, B:R.455, B:R.455, B:S.456, B:S.456, B:G.539 Water bridges: B:T.428 GOL.16: 9 residues within 4Å: Chain C: R.62, N.63, G.65, N.89, H.483, Y.485, I.488, F.489, P.490 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.483 GOL.17: 7 residues within 4Å: Chain C: P.136, V.228, N.229, L.230, V.235, E.319 Ligands: GOL.18 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.136, C:L.230 GOL.18: 8 residues within 4Å: Chain C: E.137, I.138, R.139, G.227, V.228, F.263, D.315 Ligands: GOL.17 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:I.138, C:I.138, C:V.228 Water bridges: C:S.96, C:S.96 GOL.19: 7 residues within 4Å: Chain C: I.70, G.71, R.75, L.93, Y.102, H.103, T.106 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.94, C:T.106, C:T.106 GOL.23: 10 residues within 4Å: Chain D: R.62, N.63, T.64, G.65, N.89, H.483, Y.485, I.488, F.489, P.490 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.483, D:I.488 GOL.24: 9 residues within 4Å: Chain D: P.136, I.138, V.228, N.229, L.230, V.235, F.263, R.265, E.319 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:P.136, D:L.230, D:R.265, D:E.319 Water bridges: D:I.138 GOL.25: 6 residues within 4Å: Chain D: T.451, Q.452, S.453, R.455, S.456, G.539 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:T.451, D:Q.452, D:S.453, D:R.455, D:R.455, D:S.456, D:S.456, D:G.539 Water bridges: D:T.541

4 x OXL: OXALATE ION(Non-covalent)

OXL.5: 9 residues within 4Å: Chain A: R.92, K.289, E.291, A.312, R.313, G.314, D.315, T.347 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:E.291, A:G.314, A:D.315, A:T.347, A:T.347, A:T.347 Water bridges: A:R.92, A:K.289 Salt bridges: A:R.92, A:K.289, A:K.289 OXL.11: 9 residues within 4Å: Chain B: K.289, E.291, M.310, A.312, R.313, G.314, D.315, T.347 Ligands: MG.12 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.314, B:D.315, B:D.315, B:T.347, B:T.347, B:T.347 Water bridges: B:S.262 Salt bridges: B:R.92, B:K.289 OXL.20: 9 residues within 4Å: Chain C: R.92, K.289, E.291, A.312, R.313, G.314, D.315, T.347 Ligands: MG.21 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.314, C:D.315, C:T.347, C:T.347 Water bridges: C:R.92, C:K.289 Salt bridges: C:R.92, C:K.289, C:K.289 OXL.26: 9 residues within 4Å: Chain D: K.289, E.291, M.310, A.312, R.313, G.314, D.315, T.347 Ligands: MG.27 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.314, D:D.315, D:T.347, D:T.347 Water bridges: D:S.262 Salt bridges: D:R.92, D:K.289

4 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: E.291, D.315 Ligands: OXL.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.291, A:D.315, H2O.3, H2O.4 MG.12: 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.10, H2O.11 MG.21: 3 residues within 4Å: Chain C: E.291, D.315 Ligands: OXL.20 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.291, C:D.315, H2O.18, H2O.19 MG.27: 3 residues within 4Å: Chain D: E.291, D.315 Ligands: OXL.26 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.291, D:D.315, H2O.25, H2O.26

4 x NO3: NITRATE ION(Non-functional Binders)

NO3.7: 8 residues within 4Å: Chain A: F.95, H.97, G.98, T.99, H.100, H.103, K.243, D.247 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.100, A:H.103, A:K.243 NO3.13: 7 residues within 4Å: Chain A: K.330 Chain B: F.45, H.48, M.49, L.52, L.372, A.407 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:Y.409, A:K.330, A:D.373 NO3.22: 8 residues within 4Å: Chain C: F.95, H.97, G.98, T.99, H.100, H.103, K.243, D.247 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.100, C:H.103, C:K.243 NO3.28: 7 residues within 4Å: Chain C: K.330 Chain D: F.45, H.48, M.49, L.52, L.372, A.407 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Water bridges: C:K.330, C:D.373, D:Y.409

2 x K: POTASSIUM ION(Non-covalent)

K.14: 4 residues within 4Å: Chain B: I.70, Y.102, H.103, T.106 No protein-ligand interaction detected (PLIP) K.29: 4 residues within 4Å: Chain D: I.70, Y.102, H.103, T.106 No protein-ligand interaction detected (PLIP)

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

CL.15: 2 residues within 4Å: Chain B: N.542 Chain C: V.547 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain A: V.547 Chain D: N.542 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

2020-10-07

Peptides

Pyruvate kinase PKM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Pyruvate kinase PKM