- 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)
- 8 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.3, H2O.6
MG.8: 3 residues within 4Å:- Chain B: E.270, D.294
- Ligands: OXL.12
4 PLIP interactions:2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:E.270, B:D.294, H2O.23, H2O.24
MG.9: 2 residues within 4Å:- Chain B: D.173
- Ligands: UDP.10
No protein-ligand interaction detected (PLIP)MG.14: 1 residues within 4Å:- Ligands: UDP.16
No protein-ligand interaction detected (PLIP)MG.15: 3 residues within 4Å:- Chain C: E.270, D.294
- Ligands: OXL.18
4 PLIP interactions:2 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:E.270, C:D.294, H2O.35, H2O.38
MG.20: 3 residues within 4Å:- Chain D: E.270, D.294
- Ligands: OXL.24
4 PLIP interactions:2 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:E.270, D:D.294, H2O.55, H2O.56
MG.21: 2 residues within 4Å:- Chain D: D.173
- Ligands: UDP.22
No protein-ligand interaction detected (PLIP)- 4 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:R.88, A:K.204, A:N.365
- Water bridges: A:R.74, A:R.74, A:R.74, A:H.79, A:Q.85, A:R.88, A:R.88, A:R.115, A:R.115, A:D.173, A:D.173, A:G.205, 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.10: 14 residues within 4Å:- Chain B: 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.9
20 PLIP interactions:20 interactions with chain B- Hydrogen bonds: B:N.76, B:H.79, B:R.88, B:K.204
- Water bridges: B:R.74, B:R.74, B:R.74, B:H.79, B:H.79, B:Q.85, B:D.172, B:D.172, B:D.172, B:G.205, B:S.360, B:G.361
- Salt bridges: B:R.74, B:H.79, B:R.115
- pi-Stacking: B:H.79
UDP.16: 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.14
25 PLIP interactions:25 interactions with chain C- Hydrogen bonds: C:N.76, C:H.79, C:R.88, C:K.204, C:S.360, C:N.365
- Water bridges: C:R.74, C:R.74, C:R.74, C:H.79, C:Q.85, C:R.88, C:R.88, C:R.115, C:R.115, C:D.173, C:D.173, C:G.205, C:S.360, C:G.361, C:N.365
- Salt bridges: C:R.74, C:H.79, C:R.115
- pi-Stacking: C:H.79
UDP.22: 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.21
20 PLIP interactions:20 interactions with chain D- Hydrogen bonds: D:N.76, D:H.79, D:R.88, D:K.204
- Water bridges: D:R.74, D:R.74, D:R.74, D:H.79, D:H.79, D:Q.85, D:D.172, D:D.172, D:D.172, D:G.205, D:S.360, D:G.361
- Salt bridges: D:R.74, 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.5, H2O.10
K.11: 5 residues within 4Å:- Chain B: N.76, S.78, D.108, T.109, S.240
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:S.78, B:D.108, B:T.109, H2O.27, H2O.28
K.17: 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.37, H2O.42
K.23: 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.60, H2O.60
- 4 x OXL: OXALATE ION(Non-covalent)
OXL.6: 9 residues within 4Å:- Chain A: R.74, K.268, E.270, A.291, R.292, G.293, D.294, T.326
- Ligands: MG.3
12 PLIP interactions:12 interactions with chain A- Hydrogen bonds: A:E.270, A:E.270, A:E.270, A:G.293, A:D.294, A:T.326
- Water bridges: A:R.74, A:R.74, A:R.74
- Salt bridges: A:R.74, A:K.268, A:K.268
OXL.12: 9 residues within 4Å:- Chain B: D.173, K.268, E.270, A.291, R.292, G.293, D.294, T.326
- Ligands: MG.8
8 PLIP interactions:8 interactions with chain B- Hydrogen bonds: B:E.270, B:G.293, B:D.294
- Water bridges: B:R.74, B:R.74
- Salt bridges: B:R.74, B:K.268, B:K.268
OXL.18: 9 residues within 4Å:- Chain C: R.74, K.268, E.270, A.291, R.292, G.293, D.294, T.326
- Ligands: MG.15
13 PLIP interactions:13 interactions with chain C- Hydrogen bonds: C:E.270, 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.24: 9 residues within 4Å:- Chain D: D.173, K.268, E.270, A.291, R.292, G.293, D.294, T.326
- Ligands: MG.20
8 PLIP interactions:8 interactions with chain D- Hydrogen bonds: D:E.270, D:G.293, D:D.294
- Water bridges: D:R.74, D:R.74
- Salt bridges: D:R.74, D:K.268, 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
AB
BC
AD
B
- 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)
- 8 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
- 4 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
AB
BC
AD
B