- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.80 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)
- 4 x OXL: OXALATE ION(Non-covalent)
OXL.2: 9 residues within 4Å:- Chain A: K.306, E.308, A.329, R.330, G.331, D.332, T.364, M.396
- Ligands: MG.4
9 PLIP interactions:9 interactions with chain A- Hydrogen bonds: A:E.308, A:G.331, A:D.332, A:T.364, A:T.364
- Water bridges: A:K.306
- Salt bridges: A:R.109, A:K.306, A:K.306
OXL.12: 9 residues within 4Å:- Chain B: K.306, E.308, A.329, R.330, G.331, D.332, T.364, M.396
- Ligands: MG.14
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:G.331, B:D.332, B:T.364
- Water bridges: B:R.109
- Salt bridges: B:R.109, B:K.306, B:K.306
OXL.21: 7 residues within 4Å:- Chain C: K.306, E.308, A.329, G.331, D.332, T.364
- Ligands: MG.23
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:G.331, C:D.332, C:T.364, C:T.364
- Salt bridges: C:R.109, C:K.306, C:K.306
OXL.32: 8 residues within 4Å:- Chain D: K.306, E.308, A.329, R.330, G.331, D.332, T.364
- Ligands: MG.34
11 PLIP interactions:11 interactions with chain D- Hydrogen bonds: D:E.308, D:E.308, D:G.331, D:D.332, D:D.332, D:T.364, D:T.364
- Water bridges: D:R.109
- Salt bridges: D:R.109, D:K.306, D:K.306
- 4 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.3: 4 residues within 4Å:- Chain A: N.111, S.113, H.114, R.156
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:N.111, A:S.113
- Salt bridges: A:H.114, A:R.156
PO4.13: 3 residues within 4Å:- Chain B: N.111, H.114, R.156
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:N.111
- Salt bridges: B:H.114, B:R.156
PO4.22: 3 residues within 4Å:- Chain C: N.111, H.114, R.156
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:N.111
- Salt bridges: C:H.114, C:R.156
PO4.33: 3 residues within 4Å:- Chain D: N.111, H.114, R.156
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:N.111
- Salt bridges: D:H.114, D:R.156
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.4: 3 residues within 4Å:- Chain A: E.308, D.332
- Ligands: OXL.2
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:E.308, A:D.332, H2O.1
MG.14: 4 residues within 4Å:- Chain B: K.306, E.308, D.332
- Ligands: OXL.12
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:E.308, B:D.332
MG.23: 4 residues within 4Å:- Chain C: K.306, E.308, D.332
- Ligands: OXL.21
2 PLIP interactions:2 interactions with chain C- Metal complexes: C:E.308, C:D.332
MG.34: 3 residues within 4Å:- Chain D: E.308, D.332
- Ligands: OXL.32
2 PLIP interactions:2 interactions with chain D- Metal complexes: D:E.308, D:D.332
- 4 x K: POTASSIUM ION(Non-covalent)
K.5: 6 residues within 4Å:- Chain A: N.111, S.113, D.149, T.150, S.279, K.306
No protein-ligand interaction detected (PLIP)K.15: 5 residues within 4Å:- Chain B: N.111, S.113, D.149, T.150, S.279
No protein-ligand interaction detected (PLIP)K.24: 4 residues within 4Å:- Chain C: N.111, S.113, D.149, T.150
1 PLIP interactions:1 interactions with chain C- Metal complexes: C:D.149
K.35: 6 residues within 4Å:- Chain D: N.111, S.113, D.149, T.150, E.154, S.279
No protein-ligand interaction detected (PLIP)- 20 x GOL: GLYCEROL(Non-functional Binders)
GOL.6: 3 residues within 4Å:- Chain A: H.114, G.115, K.242
Ligand excluded by PLIPGOL.7: 5 residues within 4Å:- Chain A: W.518, A.519, D.523, T.549, G.550
Ligand excluded by PLIPGOL.8: 6 residues within 4Å:- Chain A: P.153, E.154, I.155, V.252, F.280, E.336
Ligand excluded by PLIPGOL.9: 6 residues within 4Å:- Chain A: R.79, K.102, S.103, G.104, R.142, N.415
Ligand excluded by PLIPGOL.10: 4 residues within 4Å:- Chain A: E.321, S.323, D.324, K.358
Ligand excluded by PLIPGOL.16: 3 residues within 4Å:- Chain B: H.114, G.115, K.242
Ligand excluded by PLIPGOL.17: 5 residues within 4Å:- Chain B: W.518, A.519, V.522, D.523, G.550
Ligand excluded by PLIPGOL.18: 6 residues within 4Å:- Chain B: R.79, K.102, S.103, R.142, N.415, R.536
Ligand excluded by PLIPGOL.19: 5 residues within 4Å:- Chain B: R.291, E.321, A.322, D.324, K.358
Ligand excluded by PLIPGOL.25: 3 residues within 4Å:- Chain C: H.114, G.115, K.242
Ligand excluded by PLIPGOL.26: 4 residues within 4Å:- Chain C: W.518, D.523, T.549, R.562
Ligand excluded by PLIPGOL.27: 7 residues within 4Å:- Chain C: P.153, V.245, N.246, L.247, V.252, F.280, E.336
Ligand excluded by PLIPGOL.28: 8 residues within 4Å:- Chain C: C.353, N.354, G.357, K.358, D.393, R.479, R.481, Y.502
Ligand excluded by PLIPGOL.29: 7 residues within 4Å:- Chain C: R.79, K.102, S.103, G.104, R.142, N.415, R.536
Ligand excluded by PLIPGOL.30: 6 residues within 4Å:- Chain C: R.291, E.321, A.322, S.323, D.324, K.358
Ligand excluded by PLIPGOL.36: 3 residues within 4Å:- Chain D: H.114, G.115, K.242
Ligand excluded by PLIPGOL.37: 5 residues within 4Å:- Chain D: V.522, D.523, T.549, G.550, R.562
Ligand excluded by PLIPGOL.38: 7 residues within 4Å:- Chain D: P.153, V.245, N.246, L.247, V.252, F.280, E.336
Ligand excluded by PLIPGOL.39: 6 residues within 4Å:- Chain D: R.79, K.102, S.103, G.104, R.142, N.415
Ligand excluded by PLIPGOL.40: 6 residues within 4Å:- Chain D: R.291, E.321, A.322, S.323, D.324, K.358
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Dombrauckas, J.D. et al., Structural basis for tumor pyruvate kinase M2 allosteric regulation and catalysis. Biochemistry (2005)
- Release Date
- 2005-07-12
- Peptides
- Pyruvate kinase, M2 isozyme: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.80 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)
- 4 x OXL: OXALATE ION(Non-covalent)
- 4 x PO4: PHOSPHATE ION(Non-functional Binders)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 4 x K: POTASSIUM ION(Non-covalent)
- 20 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Dombrauckas, J.D. et al., Structural basis for tumor pyruvate kinase M2 allosteric regulation and catalysis. Biochemistry (2005)
- Release Date
- 2005-07-12
- Peptides
- Pyruvate kinase, M2 isozyme: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D