SMTL ID : 7l21.1

Pyruvate Kinase M2 mutant-N70D

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-tetramer

Ligands

4 x OXL: OXALATE ION(Non-covalent)

OXL.1: 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.314, A:D.315 Salt bridges: A:R.92, A:K.289, A:K.289 OXL.7: 9 residues within 4Å: Chain B: R.92, K.289, E.291, A.312, R.313, G.314, D.315, T.347 Ligands: MG.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.291, B:G.314, B:D.315, B:D.315, B:T.347 Water bridges: B:K.289 Salt bridges: B:R.92, B:K.289 OXL.13: 9 residues within 4Å: Chain C: R.92, K.289, E.291, A.312, R.313, G.314, D.315, T.347 Ligands: MG.14 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.291, C:G.314, C:D.315, C:T.347 Salt bridges: C:R.92, C:K.289 OXL.19: 9 residues within 4Å: Chain D: R.92, K.289, E.291, A.312, R.313, G.314, D.315, T.347 Ligands: MG.20 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:E.291, D:G.314, D:D.315, D:D.315, D:D.315, D:T.347 Water bridges: D:R.92, D:K.289 Salt bridges: D:R.92, D:K.289

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.289, E.291, D.315 Ligands: OXL.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.291, A:D.315 MG.8: 3 residues within 4Å: Chain B: E.291, D.315 Ligands: OXL.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.291, B:D.315, H2O.6, H2O.9 MG.14: 3 residues within 4Å: Chain C: E.291, D.315 Ligands: OXL.13 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.291, C:D.315, H2O.14, H2O.14 MG.20: 4 residues within 4Å: Chain D: K.289, E.291, D.315 Ligands: OXL.19 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.291, D:D.315, H2O.20, H2O.21

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain A: R.62, N.63, T.64, G.65, D.89, D.376, H.483, Y.485, R.486, G.487, I.488 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.62, A:G.65, A:H.483, A:Y.485 GOL.4: 6 residues within 4Å: Chain A: R.62, K.85, S.86, G.87, H.398, R.519 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.62 Water bridges: A:H.398 GOL.5: 7 residues within 4Å: Chain A: P.136, V.228, N.229, L.230, F.263, R.265, E.319 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.136, A:L.230, A:R.265 GOL.9: 11 residues within 4Å: Chain B: R.62, N.63, T.64, G.65, D.89, D.376, H.483, Y.485, R.486, G.487, I.488 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.62, B:G.65, B:H.483, B:Y.485, B:G.487 GOL.10: 6 residues within 4Å: Chain B: R.62, K.85, G.87, R.125, H.398, R.519 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.62, B:K.85, B:R.519 Water bridges: B:S.86 GOL.11: 8 residues within 4Å: Chain B: P.136, V.228, N.229, L.230, V.235, F.263, R.265, E.319 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.136, B:L.230, B:R.265, B:R.265 GOL.15: 8 residues within 4Å: Chain C: E.137, I.138, R.139, G.227, V.228, N.229, F.263, D.315 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:I.138, C:I.138, C:R.139, C:V.228, C:D.315 GOL.16: 11 residues within 4Å: Chain C: R.62, N.63, T.64, G.65, D.89, D.376, H.483, Y.485, R.486, G.487, I.488 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.62, C:G.65, C:H.483, C:Y.485 GOL.17: 7 residues within 4Å: Chain B: D.197, L.199, Q.348 Chain C: R.358, P.359, T.360, R.361 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.358, C:R.358, C:R.361, C:R.361, B:D.197, B:Q.348 Water bridges: C:P.359 GOL.21: 8 residues within 4Å: Chain D: E.137, I.138, R.139, G.227, V.228, N.229, F.263, D.315 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:I.138, D:I.138, D:V.228, D:V.228, D:D.315 GOL.22: 10 residues within 4Å: Chain D: R.62, N.63, T.64, G.65, D.89, H.483, Y.485, G.487, I.488, P.490 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.62, D:H.483, D:Y.485, D:G.487, D:I.488 Water bridges: D:R.62, D:R.62

4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)

FBP.6: 8 residues within 4Å: Chain A: T.428, T.451, K.452, S.453, R.455, S.456, F.540, T.541 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.428 Hydrogen bonds: A:T.451, A:K.452, A:S.453, A:G.454, A:R.455, A:S.456, A:S.456, A:S.456, A:T.541 FBP.12: 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:S.456, B:S.456, B:S.456, B:S.456 FBP.18: 6 residues within 4Å: Chain C: T.451, K.452, S.453, R.455, S.456, T.541 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:T.451, C:T.451, C:K.452, C:S.453, C:S.453, C:G.454, C:R.455, C:S.456, C:S.456 FBP.23: 9 residues within 4Å: Chain D: L.450, T.451, K.452, S.453, G.454, R.455, S.456, F.540, T.541 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.451, D:T.451, D:K.452, D:S.453, D:G.454, D:R.455, D:S.456

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nandi, S. et al., Identification of residues involved in allosteric signal transmission from amino acid binding site of pyruvate kinase muscle isoform 2. Plos One (2023)

Release Date

2021-12-22

Peptides

Pyruvate kinase PKM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

C
B

D
A

Pyruvate kinase PKM