- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.99 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x K: POTASSIUM ION(Non-covalent)
- 6 x MG: MAGNESIUM ION(Non-covalent)
MG.2: 2 residues within 4Å:- Chain A: S.360
- Ligands: ATP.5
No protein-ligand interaction detected (PLIP)MG.3: 5 residues within 4Å:- Chain A: K.268, E.270, D.294
- Ligands: OXL.4, ATP.5
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:E.270, A:D.294, H2O.2
MG.8: 3 residues within 4Å:- Chain B: E.270, D.294
- Ligands: OXL.9
4 PLIP interactions:2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:E.270, B:D.294, H2O.13, H2O.14
MG.12: 2 residues within 4Å:- Chain C: S.360
- Ligands: ATP.15
No protein-ligand interaction detected (PLIP)MG.13: 5 residues within 4Å:- Chain C: K.268, E.270, D.294
- Ligands: OXL.14, ATP.15
3 PLIP interactions:2 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:E.270, C:D.294, H2O.21
MG.18: 3 residues within 4Å:- Chain D: E.270, D.294
- Ligands: OXL.19
4 PLIP interactions:2 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:E.270, D:D.294, H2O.33, H2O.34
- 4 x OXL: OXALATE ION(Non-covalent)
OXL.4: 10 residues within 4Å:- Chain A: K.268, E.270, A.291, R.292, G.293, D.294, T.326, M.358
- Ligands: MG.3, ATP.5
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:G.293, A:D.294, A:T.326, A:T.326
- Salt bridges: A:R.74, A:K.268
OXL.9: 9 residues within 4Å:- Chain B: K.268, E.270, A.291, R.292, G.293, D.294, T.326, M.358
- Ligands: MG.8
10 PLIP interactions:10 interactions with chain B- Hydrogen bonds: B:G.293, B:D.294, B:T.326, B:T.326, B:T.326
- Water bridges: B:R.74, B:K.268
- Salt bridges: B:R.74, B:K.268, B:K.268
OXL.14: 10 residues within 4Å:- Chain C: K.268, E.270, A.291, R.292, G.293, D.294, T.326, M.358
- Ligands: MG.13, ATP.15
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:G.293, C:D.294, C:T.326, C:T.326, C:T.326
- Salt bridges: C:R.74, C:K.268
OXL.19: 9 residues within 4Å:- Chain D: K.268, E.270, A.291, R.292, G.293, D.294, T.326, M.358
- Ligands: MG.18
9 PLIP interactions:9 interactions with chain D- Hydrogen bonds: D:G.293, D:D.294, D:T.326, D:T.326
- Water bridges: D:R.74, D:K.268
- Salt bridges: D:R.74, D:K.268, D:K.268
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
ATP.5: 21 residues within 4Å:- Chain A: T.30, L.31, P.33, R.74, N.76, H.79, E.84, R.88, D.108, R.115, K.204, K.268, D.294, S.360, G.361, A.364, N.365
- Ligands: K.1, MG.2, MG.3, OXL.4
21 PLIP interactions:21 interactions with chain A- Hydrogen bonds: A:N.76, A:E.84, A:R.88, A:K.204, A:K.204
- Water bridges: A:N.76, A:R.115, A:R.115, A:R.115, A:S.240, A:K.268, A:K.268, A:S.360, A:S.360
- Salt bridges: A:R.74, A:R.74, A:H.79, A:R.115, A:R.115, A:K.268
- pi-Stacking: A:H.79
ATP.15: 21 residues within 4Å:- Chain C: T.30, L.31, P.33, R.74, N.76, H.79, E.84, R.88, D.108, R.115, K.204, K.268, D.294, S.360, G.361, A.364, N.365
- Ligands: K.11, MG.12, MG.13, OXL.14
23 PLIP interactions:23 interactions with chain C- Hydrogen bonds: C:N.76, C:E.84, C:R.88, C:K.204, C:K.204
- Water bridges: C:N.76, C:H.79, C:R.115, C:R.115, C:R.115, C:S.240, C:K.268, C:K.268, C:T.326, C:S.360, C:S.360
- Salt bridges: C:R.74, C:R.74, C:H.79, C:R.115, C:R.115, C:K.268
- pi-Stacking: C:H.79
- 4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)
FBP.6: 11 residues within 4Å:- Chain A: S.402, K.403, T.404, T.427, K.428, T.429, G.430, H.431, T.432, V.510, R.511
20 PLIP interactions:20 interactions with chain A- Hydrogen bonds: A:S.402, A:K.403, A:T.404, A:T.404, A:T.427, A:T.427, A:T.427, A:K.428, A:T.429, A:G.430, A:H.431, A:T.432, A:T.432
- Water bridges: A:H.431, A:T.512, A:T.512, A:T.512, A:T.512
- Salt bridges: A:H.431, A:R.511
FBP.10: 11 residues within 4Å:- Chain B: S.402, K.403, T.404, T.427, K.428, T.429, G.430, H.431, T.432, V.510, R.511
19 PLIP interactions:19 interactions with chain B- Hydrogen bonds: B:S.402, B:K.403, B:T.404, B:T.404, B:T.404, B:T.427, B:T.427, B:K.428, B:T.429, B:G.430, B:H.431, B:T.432, B:T.432, B:V.510
- Water bridges: B:S.402, B:H.431, B:T.512
- Salt bridges: B:H.431, B:R.511
FBP.16: 11 residues within 4Å:- Chain C: S.402, K.403, T.404, T.427, K.428, T.429, G.430, H.431, T.432, V.510, R.511
17 PLIP interactions:17 interactions with chain C- Hydrogen bonds: C:S.402, C:K.403, C:T.404, C:T.404, C:T.427, C:T.427, C:K.428, C:T.429, C:G.430, C:H.431, C:T.432
- Water bridges: C:H.431, C:T.432, C:T.432, C:T.512
- Salt bridges: C:H.431, C:R.511
FBP.20: 11 residues within 4Å:- Chain D: S.402, K.403, T.404, T.427, K.428, T.429, G.430, H.431, T.432, V.510, R.511
22 PLIP interactions:22 interactions with chain D- Hydrogen bonds: D:S.402, D:K.403, D:T.404, D:T.404, D:T.404, D:T.427, D:T.427, D:T.427, D:K.428, D:T.429, D:G.430, D:H.431, D:T.432, D:V.510
- Water bridges: D:S.402, D:H.431, D:T.512, D:T.512, D:T.512, D:T.512
- Salt bridges: D:H.431, D:R.511
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Taguchi, A. et al., Structural Basis of Nucleotide Selectivity in Pyruvate Kinase. J.Mol.Biol. (2024)
- Release Date
- 2024-07-31
- Peptides
- Pyruvate kinase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.99 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x K: POTASSIUM ION(Non-covalent)
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 4 x OXL: OXALATE ION(Non-covalent)
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Taguchi, A. et al., Structural Basis of Nucleotide Selectivity in Pyruvate Kinase. J.Mol.Biol. (2024)
- Release Date
- 2024-07-31
- Peptides
- Pyruvate kinase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B