- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- homo-tetramer
- Ligands
- 11 x PO4: PHOSPHATE ION(Non-functional Binders)
- 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 PLIPGOL.8: 3 residues within 4Å:- Chain A: I.107, K.108, R.111
Ligand excluded by PLIPGOL.9: 3 residues within 4Å:- Chain A: G.145, G.147, A.149
Ligand excluded by PLIPGOL.10: 7 residues within 4Å:- Chain A: R.62, N.63, G.65, N.89, H.483, I.488, F.489
Ligand excluded by PLIPGOL.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 PLIPGOL.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 PLIPGOL.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 PLIPGOL.18: 5 residues within 4Å:- Chain B: N.94, S.96, H.97, E.137, R.139
Ligand excluded by PLIPGOL.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 PLIPGOL.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 PLIPGOL.21: 5 residues within 4Å:- Chain B: H.410, L.411, F.414, F.440
- Ligands: GOL.31
Ligand excluded by PLIPGOL.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 PLIPGOL.30: 6 residues within 4Å:- Chain C: P.136, V.228, N.229, L.230, V.235, E.319
Ligand excluded by PLIPGOL.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 PLIPGOL.39: 6 residues within 4Å:- Chain D: R.62, G.65, N.89, H.483, I.488, F.489
Ligand excluded by PLIPGOL.40: 6 residues within 4Å:- Chain D: T.69, R.92, N.94, S.381, G.382, A.385
Ligand excluded by PLIPGOL.41: 7 residues within 4Å:- Chain D: P.136, V.228, N.229, L.230, V.235, R.265, E.319
Ligand excluded by PLIPGOL.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)
- 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
AB
CC
BD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- homo-tetramer
- Ligands
- 11 x PO4: PHOSPHATE ION(Non-functional Binders)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 5 x K: POTASSIUM ION(Non-covalent)
- 2 x OXL: OXALATE ION(Non-covalent)
- 18 x GOL: GLYCEROL(Non-functional Binders)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 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
AB
CC
BD
D