- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.41 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x PRO: PROLINE(Non-covalent)
- 4 x MN: MANGANESE (II) ION(Non-covalent)
MN.2: 3 residues within 4Å:- Chain A: E.272, D.296
- Ligands: PYR.3
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:E.272, A:D.296, H2O.7
MN.14: 3 residues within 4Å:- Chain B: E.272, D.296
- Ligands: PYR.15
4 PLIP interactions:2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:E.272, B:D.296, H2O.11, H2O.13
MN.23: 3 residues within 4Å:- Chain C: E.272, D.296
- Ligands: PYR.24
4 PLIP interactions:2 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:E.272, C:D.296, H2O.17, H2O.18
MN.30: 5 residues within 4Å:- Chain D: F.244, E.272, D.296
- Ligands: PYR.31, GOL.36
4 PLIP interactions:2 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:E.272, D:D.296, H2O.23, H2O.25
- 4 x PYR: PYRUVIC ACID(Non-covalent)
PYR.3: 9 residues within 4Å:- Chain A: K.270, E.272, M.291, A.293, R.294, G.295, D.296, T.328
- Ligands: MN.2
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:A.293
- Hydrogen bonds: A:K.270, A:G.295, A:D.296
- Salt bridges: A:K.270
PYR.15: 11 residues within 4Å:- Chain B: R.73, K.270, E.272, M.291, A.293, R.294, G.295, D.296, T.328, M.360
- Ligands: MN.14
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:K.270, B:G.295, B:D.296, B:T.328
- Salt bridges: B:K.270
PYR.24: 9 residues within 4Å:- Chain C: R.73, K.270, E.272, A.293, R.294, G.295, D.296, T.328
- Ligands: MN.23
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:K.270, C:G.295, C:D.296, C:T.328
PYR.31: 9 residues within 4Å:- Chain D: K.270, E.272, M.291, A.293, R.294, G.295, D.296, T.328
- Ligands: MN.30
8 PLIP interactions:8 interactions with chain D- Hydrogen bonds: D:K.270, D:G.295, D:D.296, D:D.296, D:D.296, D:T.328
- Water bridges: D:R.73
- Salt bridges: D:K.270
- 4 x K: POTASSIUM ION(Non-covalent)
K.4: 6 residues within 4Å:- Chain A: N.75, S.77, D.113, T.114, S.243, K.270
2 PLIP interactions:1 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.113, H2O.3
K.16: 6 residues within 4Å:- Chain B: N.75, S.77, D.113, T.114, S.243, K.270
4 PLIP interactions:3 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:S.77, B:D.113, B:T.114, H2O.14
K.25: 6 residues within 4Å:- Chain C: N.75, S.77, D.113, T.114, S.243, K.270
3 PLIP interactions:2 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:S.77, C:D.113, H2O.18
K.32: 6 residues within 4Å:- Chain D: N.75, S.77, D.113, T.114, S.243, K.270
4 PLIP interactions:3 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:S.77, D:D.113, D:T.114, H2O.22
- 6 x NA: SODIUM ION(Non-functional Binders)
NA.5: 6 residues within 4Å:- Chain A: K.125, G.126, S.127, G.128, T.129, A.130
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:G.128
NA.6: 4 residues within 4Å:- Chain A: T.432, S.434, R.436, S.437
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:T.432, A:S.434, A:R.436, A:S.437
- Water bridges: A:S.434
NA.17: 3 residues within 4Å:- Chain B: T.432, S.434, S.437
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:T.432, B:S.437, B:S.437
NA.26: 3 residues within 4Å:- Chain C: T.432, S.434, S.437
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:E.433, C:S.434
NA.33: 5 residues within 4Å:- Chain D: K.125, G.126, S.127, G.128, T.129
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:K.125
NA.34: 3 residues within 4Å:- Chain D: T.432, S.434, S.437
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:T.432, D:S.437
- 6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.7: 3 residues within 4Å:- Chain A: P.39, T.41, R.383
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:P.39, A:R.383, A:R.383
EDO.8: 3 residues within 4Å:- Chain A: D.178, G.295, D.296
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:D.178
EDO.9: 6 residues within 4Å:- Chain A: T.50, I.51, G.52, P.53, N.75, A.366
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.75, A:N.75
EDO.10: 6 residues within 4Å:- Chain A: R.255, E.285, A.286, S.287, D.288, K.322
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:A.286, A:K.322, A:K.322
EDO.19: 4 residues within 4Å:- Chain B: A.38, P.39, T.41, R.383
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:T.41, B:R.383, B:R.383
EDO.35: 5 residues within 4Å:- Chain D: E.285, A.286, S.287, D.288, K.322
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:A.286, D:K.322
- 8 x GOL: GLYCEROL(Non-functional Binders)
GOL.11: 10 residues within 4Å:- Chain A: P.117, I.119, V.209, N.210, L.211, V.216, F.244, R.246, E.300
- Ligands: GOL.12
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:P.117, A:N.210, A:L.211, A:R.246
- Water bridges: A:L.218
GOL.12: 8 residues within 4Å:- Chain A: E.118, I.119, G.208, V.209, N.210, F.244, D.296
- Ligands: GOL.11
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:E.118, A:I.119
- Water bridges: A:S.77, A:S.77
GOL.18: 6 residues within 4Å:- Chain B: D.178, Q.329
- Chain D: R.339, P.340, T.341, R.342
4 PLIP interactions:3 interactions with chain D, 1 interactions with chain B- Hydrogen bonds: D:R.342, D:R.342, B:Q.329
- Water bridges: D:P.340
GOL.20: 10 residues within 4Å:- Chain B: P.117, I.119, V.209, N.210, L.211, V.216, F.244, R.246, E.300
- Ligands: GOL.21
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:P.117, B:L.211, B:R.246, B:R.246
GOL.21: 8 residues within 4Å:- Chain B: E.118, I.119, G.208, V.209, N.210, F.244, D.296
- Ligands: GOL.20
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:E.118, B:I.119, B:R.120, B:V.209, B:D.296
GOL.27: 9 residues within 4Å:- Chain C: P.117, V.209, N.210, L.211, V.216, F.244, R.246, E.300
- Ligands: GOL.28
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:P.117, C:N.210, C:L.211, C:R.246
GOL.28: 8 residues within 4Å:- Chain C: E.118, I.119, G.208, V.209, N.210, F.244, D.296
- Ligands: GOL.27
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:I.119, C:I.119, C:V.209, C:D.296
GOL.36: 9 residues within 4Å:- Chain D: E.118, I.119, R.120, G.208, V.209, N.210, F.244, D.296
- Ligands: MN.30
6 PLIP interactions:6 interactions with chain D- Hydrogen bonds: D:I.119, D:I.119
- Water bridges: D:E.272, D:E.272, D:D.296, D:D.296
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Fenton, A.W. et al., The pyruvate kinase model system, a cautionary tale for the use of osmolyte perturbations to support conformational equilibria in allostery. Protein Sci. (2010)
- Release Date
- 2010-07-28
- Peptides
- Pyruvate kinase isozymes M1/M2: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
EB
FC
GD
H
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.41 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x PRO: PROLINE(Non-covalent)
- 4 x MN: MANGANESE (II) ION(Non-covalent)
- 4 x PYR: PYRUVIC ACID(Non-covalent)
- 4 x K: POTASSIUM ION(Non-covalent)
- 6 x NA: SODIUM ION(Non-functional Binders)
- 6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 8 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Fenton, A.W. et al., The pyruvate kinase model system, a cautionary tale for the use of osmolyte perturbations to support conformational equilibria in allostery. Protein Sci. (2010)
- Release Date
- 2010-07-28
- Peptides
- Pyruvate kinase isozymes M1/M2: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
EB
FC
GD
H