- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 4 x K: POTASSIUM ION(Non-covalent)
K.2: 6 residues within 4Å:- Chain A: N.52, S.54, D.84, T.85, S.212, K.239
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:S.54, A:D.84, A:T.85, H2O.3, H2O.4
K.6: 6 residues within 4Å:- Chain B: N.52, S.54, D.84, T.85, S.212, K.239
4 PLIP interactions:2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:D.84, B:T.85, H2O.9, H2O.12
K.13: 6 residues within 4Å:- Chain C: N.52, S.54, D.84, T.85, S.212, K.239
5 PLIP interactions:3 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:S.54, C:D.84, C:T.85, H2O.20, H2O.20
K.17: 6 residues within 4Å:- Chain D: N.52, S.54, D.84, T.85, S.212, K.239
4 PLIP interactions:2 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:D.84, D:T.85, H2O.26, H2O.29
- 4 x OXL: OXALATE ION(Non-covalent)
OXL.3: 8 residues within 4Å:- Chain A: K.239, E.241, A.262, R.263, G.264, D.265, T.297
- Ligands: MG.1
9 PLIP interactions:9 interactions with chain A- Hydrogen bonds: A:G.264, A:D.265, A:D.265, A:T.297
- Water bridges: A:R.50, A:K.239
- Salt bridges: A:R.50, A:K.239, A:K.239
OXL.7: 8 residues within 4Å:- Chain B: K.239, E.241, A.262, R.263, G.264, D.265, T.297
- Ligands: MG.5
10 PLIP interactions:10 interactions with chain B- Hydrogen bonds: B:E.241, B:G.264, B:D.265, B:D.265, B:T.297, B:T.297
- Water bridges: B:R.50, B:K.239
- Salt bridges: B:R.50, B:K.239
OXL.14: 8 residues within 4Å:- Chain C: K.239, E.241, A.262, R.263, G.264, D.265, T.297
- Ligands: MG.12
9 PLIP interactions:9 interactions with chain C- Hydrogen bonds: C:G.264, C:D.265, C:D.265, C:T.297
- Water bridges: C:R.50, C:K.239
- Salt bridges: C:R.50, C:K.239, C:K.239
OXL.18: 8 residues within 4Å:- Chain D: K.239, E.241, A.262, R.263, G.264, D.265, T.297
- Ligands: MG.16
10 PLIP interactions:10 interactions with chain D- Hydrogen bonds: D:E.241, D:G.264, D:D.265, D:D.265, D:T.297, D:T.297
- Water bridges: D:R.50, D:K.239
- Salt bridges: D:R.50, D:K.239
- 4 x FDP: 2,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)
FDP.4: 15 residues within 4Å:- Chain A: L.400, S.401, N.402, T.403, R.405, S.406, K.454, R.457, H.481, A.482, V.486, K.487, G.488, Y.489, P.490
12 PLIP interactions:12 interactions with chain A- Hydrogen bonds: A:N.402, A:N.402, A:T.403, A:S.406, A:S.406, A:K.454, A:A.482, A:V.486, A:G.488
- Water bridges: A:S.406
- Salt bridges: A:K.454, A:R.457
FDP.8: 15 residues within 4Å:- Chain B: L.400, S.401, N.402, T.403, R.405, S.406, K.454, R.457, H.481, A.482, V.486, K.487, G.488, Y.489, P.490
16 PLIP interactions:16 interactions with chain B- Hydrogen bonds: B:N.402, B:N.402, B:T.403, B:G.404, B:R.405, B:S.406, B:S.406, B:K.454, B:A.482, B:V.486, B:G.488
- Water bridges: B:R.405, B:K.454, B:K.487
- Salt bridges: B:K.454, B:R.457
FDP.15: 15 residues within 4Å:- Chain C: L.400, S.401, N.402, T.403, R.405, S.406, K.454, R.457, H.481, A.482, V.486, K.487, G.488, Y.489, P.490
12 PLIP interactions:12 interactions with chain C- Hydrogen bonds: C:N.402, C:N.402, C:T.403, C:S.406, C:S.406, C:K.454, C:A.482, C:V.486, C:G.488
- Water bridges: C:S.406
- Salt bridges: C:K.454, C:R.457
FDP.19: 15 residues within 4Å:- Chain D: L.400, S.401, N.402, T.403, R.405, S.406, K.454, R.457, H.481, A.482, V.486, K.487, G.488, Y.489, P.490
16 PLIP interactions:16 interactions with chain D- Hydrogen bonds: D:N.402, D:N.402, D:T.403, D:G.404, D:R.405, D:S.406, D:S.406, D:K.454, D:A.482, D:V.486, D:G.488
- Water bridges: D:R.405, D:K.454, D:K.487
- Salt bridges: D:K.454, D:R.457
- 6 x GOL: GLYCEROL(Non-functional Binders)
GOL.9: 6 residues within 4Å:- Chain B: C.429, L.432, N.433, V.438, V.439, S.440
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:C.429, B:N.433, B:S.440, B:S.440
- Water bridges: B:R.23
GOL.10: 9 residues within 4Å:- Chain B: P.88, I.90, I.178, N.179, L.180, V.185, F.213, R.215, E.269
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:P.88, B:L.180, B:R.215, B:R.215
- Water bridges: B:N.242
GOL.11: 4 residues within 4Å:- Chain B: A.17, K.18, H.19, Q.355
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:K.18, B:H.19, B:H.19, B:Q.355
- Water bridges: B:V.16
GOL.20: 6 residues within 4Å:- Chain D: C.429, L.432, N.433, V.438, V.439, S.440
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:C.429, D:N.433, D:S.440, D:S.440
- Water bridges: D:R.23
GOL.21: 9 residues within 4Å:- Chain D: P.88, I.90, I.178, N.179, L.180, V.185, F.213, R.215, E.269
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:P.88, D:L.180, D:R.215, D:R.215
- Water bridges: D:N.242
GOL.22: 4 residues within 4Å:- Chain D: A.17, K.18, H.19, Q.355
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:K.18, D:H.19, D:H.19, D:Q.355
- Water bridges: D:V.16
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhong, W. et al., Pyruvate kinases have an intrinsic and conserved decarboxylase activity. Biochem.J. (2014)
- Release Date
- 2014-01-08
- Peptides
- Pyruvate kinase 1: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 4 x K: POTASSIUM ION(Non-covalent)
- 4 x OXL: OXALATE ION(Non-covalent)
- 4 x FDP: 2,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)
- 6 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhong, W. et al., Pyruvate kinases have an intrinsic and conserved decarboxylase activity. Biochem.J. (2014)
- Release Date
- 2014-01-08
- Peptides
- Pyruvate kinase 1: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B