- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
- 4 x K: POTASSIUM ION(Non-covalent)
K.3: 5 residues within 4Å:- Chain A: N.76, S.78, D.108, T.109, S.240
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:S.78, A:D.108, A:T.109, H2O.10, H2O.14
K.11: 5 residues within 4Å:- Chain B: N.76, S.78, D.108, T.109, S.240
4 PLIP interactions:2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:D.108, B:T.109, H2O.31, H2O.31
K.18: 5 residues within 4Å:- Chain C: N.76, S.78, D.108, T.109, S.240
5 PLIP interactions:3 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:S.78, C:D.108, C:T.109, H2O.45, H2O.49
K.26: 5 residues within 4Å:- Chain D: N.76, S.78, D.108, T.109, S.240
4 PLIP interactions:2 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:D.108, D:T.109, H2O.67, H2O.67
- 4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)
FBP.4: 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
19 PLIP interactions:19 interactions with chain A- Hydrogen bonds: A:S.402, A:K.403, A:T.404, A:T.404, A:T.404, A:T.427, A:T.427, A:K.428, A:T.429, A:G.430, A:H.431, A:T.432, A:V.510
- Water bridges: A:V.510, A:R.511, A:R.511, A:T.512
- Salt bridges: A:H.431, A:R.511
FBP.12: 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
24 PLIP interactions:24 interactions with chain B- Hydrogen bonds: B:S.402, B:K.403, B:T.404, B:T.404, B:T.427, 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:V.510, B:V.510, B:R.511, B:T.512, B:T.512, B:T.512, B:T.512
- Salt bridges: B:H.431, B:R.511
FBP.19: 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
24 PLIP interactions:24 interactions with chain C- Hydrogen bonds: C:S.402, C:K.403, C:T.404, C:T.404, C:T.404, C:T.427, C:T.427, C:T.427, C:K.428, C:T.429, C:G.430, C:H.431, C:T.432, C:T.432, C:V.510
- Water bridges: C:V.510, C:R.511, C:R.511, C:T.512, C:T.512, C:T.512, C:T.512
- Salt bridges: C:H.431, C:R.511
FBP.27: 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
19 PLIP interactions:19 interactions with chain D- Hydrogen bonds: D:S.402, D:K.403, D:T.404, D:T.404, 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:V.510, D:V.510, D:R.511, D:T.512
- Salt bridges: D:H.431, D:R.511
- 4 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)
GDP.5: 16 residues within 4Å:- Chain A: T.30, L.31, P.33, R.74, N.76, H.79, E.84, Q.85, R.88, R.115, K.204, S.360, G.361, A.364, N.365
- Ligands: MG.1
27 PLIP interactions:27 interactions with chain A- Hydrogen bonds: A:N.76, A:Q.85, A:R.88, A:K.204, A:K.204
- Water bridges: A:R.74, A:R.74, A:R.74, A:N.76, A:N.76, A:E.84, A:E.84, A:E.84, A:E.84, A:R.115, A:R.115, A:D.172, A:D.172, A:K.204, A:S.360, A:G.361, A:N.365
- Salt bridges: A:R.74, A:H.79, A:E.84, A:R.115
- pi-Stacking: A:H.79
GDP.13: 16 residues within 4Å:- Chain B: T.30, P.33, W.49, R.74, N.76, H.79, G.80, E.84, Q.85, R.88, R.115, K.204, S.360, G.361, N.365
- Ligands: MG.9
21 PLIP interactions:21 interactions with chain B- Hydrogen bonds: B:N.76, B:G.80, B:Q.85, B:R.88, B:R.88, B:K.204, B:S.360, B:N.365
- Water bridges: B:R.74, B:N.76, B:E.84, B:E.84, B:R.115, B:R.115, B:R.115, B:G.361
- Salt bridges: B:R.74, B:H.79, B:E.84, B:R.115
- pi-Stacking: B:H.79
GDP.20: 16 residues within 4Å:- Chain C: T.30, L.31, P.33, R.74, N.76, H.79, E.84, Q.85, R.88, R.115, K.204, S.360, G.361, A.364, N.365
- Ligands: MG.16
28 PLIP interactions:28 interactions with chain C- Hydrogen bonds: C:N.76, C:Q.85, C:R.88, C:K.204, C:K.204
- Water bridges: C:R.74, C:R.74, C:R.74, C:N.76, C:N.76, C:E.84, C:E.84, C:E.84, C:E.84, C:R.115, C:R.115, C:R.115, C:D.172, C:K.204, C:T.326, C:S.360, C:G.361, C:N.365
- Salt bridges: C:R.74, C:H.79, C:E.84, C:R.115
- pi-Stacking: C:H.79
GDP.28: 16 residues within 4Å:- Chain D: T.30, P.33, W.49, R.74, N.76, H.79, G.80, E.84, Q.85, R.88, R.115, K.204, S.360, G.361, N.365
- Ligands: MG.24
21 PLIP interactions:21 interactions with chain D- Hydrogen bonds: D:N.76, D:G.80, D:Q.85, D:R.88, D:R.88, D:K.204, D:S.360, D:N.365
- Water bridges: D:R.74, D:N.76, D:E.84, D:E.84, D:R.115, D:R.115, D:R.115, D:G.361
- Salt bridges: D:R.74, D:H.79, D:E.84, D:R.115
- pi-Stacking: D:H.79
- 4 x OXL: OXALATE ION(Non-covalent)
OXL.6: 8 residues within 4Å:- Chain A: K.268, E.270, A.291, R.292, G.293, D.294, T.326
- Ligands: MG.2
8 PLIP interactions:8 interactions with chain A- Hydrogen bonds: A:E.270, A:G.293, A:D.294
- Water bridges: A:R.74, A:R.74, A:R.74
- Salt bridges: A:R.74, A:K.268
OXL.14: 9 residues within 4Å:- Chain B: R.74, K.268, E.270, A.291, R.292, G.293, D.294, T.326
- Ligands: MG.10
9 PLIP interactions:9 interactions with chain B- Hydrogen bonds: B:G.293, B:D.294, B:T.326, B:T.326, B:T.326
- Water bridges: B:K.268, B:K.268
- Salt bridges: B:R.74, B:K.268
OXL.21: 8 residues within 4Å:- Chain C: K.268, E.270, A.291, R.292, G.293, D.294, T.326
- Ligands: MG.17
10 PLIP interactions:10 interactions with chain C- Hydrogen bonds: C:E.270, C:E.270, C:G.293, C:D.294, C:T.326
- Water bridges: C:R.74, C:R.74, C:R.74
- Salt bridges: C:R.74, C:K.268
OXL.29: 9 residues within 4Å:- Chain D: R.74, K.268, E.270, A.291, R.292, G.293, D.294, T.326
- Ligands: MG.25
8 PLIP interactions:8 interactions with chain D- Hydrogen bonds: D:G.293, D:D.294, D:T.326, D:T.326
- Water bridges: D:K.268, D:K.268
- Salt bridges: D:R.74, D:K.268
- 6 x GOL: GLYCEROL(Non-functional Binders)
GOL.7: 6 residues within 4Å:- Chain A: A.317, A.318, G.319, N.401, E.405, K.438
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:A.318, A:E.405
- Water bridges: A:E.405, A:K.438
GOL.8: 5 residues within 4Å:- Chain A: T.415, S.416, S.417, M.418, D.419
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:S.417
- Water bridges: A:I.420, A:I.420, A:I.420
GOL.15: 6 residues within 4Å:- Chain B: A.317, A.318, G.319, N.401, E.405, K.438
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:A.318, B:E.405
- Water bridges: B:K.438
GOL.22: 6 residues within 4Å:- Chain C: A.317, A.318, G.319, N.401, E.405, K.438
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:A.318, C:E.405
- Water bridges: C:K.438
GOL.23: 5 residues within 4Å:- Chain C: T.415, S.416, S.417, M.418, D.419
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:S.417
- Water bridges: C:I.420, C:I.420, C:I.420
GOL.30: 6 residues within 4Å:- Chain D: A.317, A.318, G.319, N.401, E.405, K.438
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:A.318, D:E.405
- Water bridges: D:E.405, D:K.438
- 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
BB
CC
BD
C
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
- 4 x K: POTASSIUM ION(Non-covalent)
- 4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)
- 4 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)
- 4 x OXL: OXALATE ION(Non-covalent)
- 6 x GOL: GLYCEROL(Non-functional Binders)
- 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
BB
CC
BD
C