- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.89 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)
- 7 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
MG.2: 1 residues within 4Å:- Ligands: UDP.4
No protein-ligand interaction detected (PLIP)MG.3: 3 residues within 4Å:- Chain A: E.270, D.294
- Ligands: OXL.6
4 PLIP interactions:2 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:E.270, A:D.294, H2O.2, H2O.5
MG.8: 3 residues within 4Å:- Chain B: E.270, D.294
- Ligands: OXL.10
4 PLIP interactions:2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:E.270, B:D.294, H2O.25, H2O.25
MG.12: 1 residues within 4Å:- Ligands: UDP.14
No protein-ligand interaction detected (PLIP)MG.13: 3 residues within 4Å:- Chain C: E.270, D.294
- Ligands: OXL.16
4 PLIP interactions:2 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:E.270, C:D.294, H2O.43, H2O.44
MG.18: 1 residues within 4Å:- Ligands: UDP.20
No protein-ligand interaction detected (PLIP)MG.19: 3 residues within 4Å:- Chain D: E.270, D.294
- Ligands: OXL.22
4 PLIP interactions:2 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:E.270, D:D.294, H2O.61, H2O.63
- 3 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)
UDP.4: 14 residues within 4Å:- Chain A: T.30, L.31, P.33, R.74, N.76, H.79, R.88, R.115, K.204, S.360, G.361, A.364, N.365
- Ligands: MG.2
24 PLIP interactions:24 interactions with chain A- Hydrogen bonds: A:N.76, A:H.79, A:Q.85, A:R.88, A:K.204, A:N.365
- Water bridges: A:R.74, A:R.74, A:R.74, A:E.84, A:E.84, A:R.88, A:R.88, A:R.115, A:R.115, A:R.115, A:D.173, A:S.360, A:G.361, A:N.365
- Salt bridges: A:R.74, A:H.79, A:R.115
- pi-Stacking: A:H.79
UDP.14: 14 residues within 4Å:- Chain C: T.30, L.31, P.33, R.74, N.76, H.79, R.88, R.115, K.204, S.360, G.361, A.364, N.365
- Ligands: MG.12
25 PLIP interactions:25 interactions with chain C- Hydrogen bonds: C:N.76, C:H.79, C:Q.85, C:R.88, C:K.204, C:N.365
- Water bridges: C:R.74, C:R.74, C:N.76, C:R.88, C:R.88, C:R.115, C:R.115, C:D.172, C:D.172, C:D.172, C:T.326, C:S.360, C:G.361, C:N.365
- Salt bridges: C:R.74, C:H.79, C:H.79, C:R.115
- pi-Stacking: C:H.79
UDP.20: 14 residues within 4Å:- Chain D: T.30, L.31, P.33, R.74, N.76, H.79, R.88, R.115, K.204, S.360, G.361, A.364, N.365
- Ligands: MG.18
21 PLIP interactions:21 interactions with chain D- Hydrogen bonds: D:N.76, D:H.79, D:K.204, D:N.365
- Water bridges: D:R.74, D:R.74, D:Q.85, D:R.88, D:R.88, D:R.88, D:R.115, D:D.172, D:D.173, D:S.360, D:G.361, D:N.365
- Salt bridges: D:R.74, D:H.79, D:H.79, D:R.115
- pi-Stacking: D:H.79
- 4 x K: POTASSIUM ION(Non-covalent)
K.5: 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.9, H2O.13
K.9: 6 residues within 4Å:- Chain B: N.76, S.78, D.108, T.109, S.240, K.268
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:S.78, B:D.108, B:T.109, H2O.26, H2O.34
K.15: 5 residues within 4Å:- Chain C: N.76, S.78, D.108, T.109, S.240
4 PLIP interactions:3 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:S.78, C:D.108, C:T.109, H2O.46
K.21: 5 residues within 4Å:- Chain D: N.76, S.78, D.108, T.109, S.240
5 PLIP interactions:3 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:S.78, D:D.108, D:T.109, H2O.65, H2O.66
- 4 x OXL: OXALATE ION(Non-covalent)
OXL.6: 9 residues within 4Å:- Chain A: K.268, E.270, A.291, R.292, G.293, D.294, T.326, M.358
- Ligands: MG.3
9 PLIP interactions:9 interactions with chain A- Hydrogen bonds: A:G.293, A:D.294
- Water bridges: A:R.74, A:R.74, A:K.268, A:E.270
- Salt bridges: A:R.74, A:K.268, A:K.268
OXL.10: 8 residues within 4Å:- Chain B: K.268, E.270, A.291, R.292, G.293, D.294, T.326
- Ligands: MG.8
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:E.270, B:E.270, B:G.293, B:D.294
- Water bridges: B:R.74
- Salt bridges: B:R.74, B:K.268
OXL.16: 8 residues within 4Å:- Chain C: K.268, E.270, A.291, R.292, G.293, D.294, T.326
- Ligands: MG.13
12 PLIP interactions:12 interactions with chain C- Hydrogen bonds: C:G.293, C:D.294, C:D.294, C:D.294, 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, C:K.268
OXL.22: 8 residues within 4Å:- Chain D: K.268, E.270, A.291, R.292, G.293, D.294, T.326
- Ligands: MG.19
10 PLIP interactions:10 interactions with chain D- Hydrogen bonds: D:E.270, D:E.270, D:G.293, D:D.294, D:T.326
- Water bridges: D:R.74, D:R.74, D:R.74
- Salt bridges: D:R.74, D:K.268
- 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
GB
HC
ED
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.89 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)
- 7 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
- 3 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)
- 4 x K: POTASSIUM ION(Non-covalent)
- 4 x OXL: OXALATE ION(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
GB
HC
ED
F