- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 4 x K: POTASSIUM ION(Non-covalent)
K.2: 8 residues within 4Å:- Chain A: N.52, S.54, D.84, T.85, E.89, S.212, K.239
- Ligands: PEP.3
5 PLIP interactions:3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions- Metal complexes: A:S.54, A:D.84, A:T.85, PEP.3, H2O.7
K.7: 7 residues within 4Å:- Chain B: N.52, S.54, D.84, T.85, S.212, K.239
- Ligands: PEP.8
4 PLIP interactions:2 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions- Metal complexes: B:D.84, B:T.85, PEP.8, H2O.20
K.12: 8 residues within 4Å:- Chain C: N.52, S.54, D.84, T.85, E.89, S.212, K.239
- Ligands: PEP.13
5 PLIP interactions:3 interactions with chain C, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions- Metal complexes: C:S.54, C:D.84, C:T.85, PEP.13, H2O.40
K.17: 7 residues within 4Å:- Chain D: N.52, S.54, D.84, T.85, S.212, K.239
- Ligands: PEP.18
4 PLIP interactions:2 interactions with chain D, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions- Metal complexes: D:D.84, D:T.85, PEP.18, H2O.53
- 4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)
PEP.3: 14 residues within 4Å:- Chain A: R.50, D.84, K.239, E.241, M.260, A.262, R.263, G.264, D.265, A.296, T.297, M.329
- Ligands: MG.1, K.2
13 PLIP interactions:13 interactions with chain A- Hydrophobic interactions: A:A.296
- Hydrogen bonds: A:G.264, A:D.265, A:T.297
- Water bridges: A:S.54, A:S.212, A:K.239, A:K.239, A:S.331, A:S.331, A:S.331
- Salt bridges: A:R.50, A:K.239
PEP.8: 13 residues within 4Å:- Chain B: R.50, D.84, K.239, E.241, M.260, A.262, R.263, G.264, D.265, T.297, M.329
- Ligands: MG.6, K.7
12 PLIP interactions:12 interactions with chain B- Hydrogen bonds: B:G.264, B:D.265, B:T.297, B:T.297
- Water bridges: B:R.50, B:N.52, B:N.52, B:S.212, B:K.239, B:K.239
- Salt bridges: B:R.50, B:K.239
PEP.13: 14 residues within 4Å:- Chain C: R.50, D.84, K.239, E.241, M.260, A.262, R.263, G.264, D.265, A.296, T.297, M.329
- Ligands: MG.11, K.12
13 PLIP interactions:13 interactions with chain C- Hydrophobic interactions: C:A.296
- Hydrogen bonds: C:G.264, C:D.265, C:T.297
- Water bridges: C:S.54, C:S.212, C:K.239, C:K.239, C:S.331, C:S.331, C:S.331
- Salt bridges: C:R.50, C:K.239
PEP.18: 13 residues within 4Å:- Chain D: R.50, D.84, K.239, E.241, M.260, A.262, R.263, G.264, D.265, T.297, M.329
- Ligands: MG.16, K.17
12 PLIP interactions:12 interactions with chain D- Hydrogen bonds: D:G.264, D:D.265, D:T.297, D:T.297
- Water bridges: D:R.50, D:N.52, D:N.52, D:S.212, D:K.239, 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
17 PLIP interactions:17 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, A:Y.489
- Water bridges: A:T.424, A:R.457, A:R.457, A:R.457, A:K.487
- Salt bridges: A:K.454, A:R.457
FDP.9: 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
17 PLIP interactions:17 interactions with chain B- Hydrogen bonds: B:S.401, B:N.402, B:N.402, B:T.403, B:S.406, B:S.406, B:K.454, B:A.482, B:V.486, B:G.488, B:Y.489
- Water bridges: B:N.402, B:R.405, B:K.487, B:K.487
- Salt bridges: B:K.454, B:R.457
FDP.14: 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
17 PLIP interactions:17 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, C:Y.489
- Water bridges: C:T.424, C:R.457, C:R.457, C:R.457, C:K.487
- 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
17 PLIP interactions:17 interactions with chain D- Hydrogen bonds: D:S.401, D:N.402, D:N.402, D:T.403, D:S.406, D:S.406, D:K.454, D:A.482, D:V.486, D:G.488, D:Y.489
- Water bridges: D:N.402, D:R.405, D:K.487, D:K.487
- Salt bridges: D:K.454, D:R.457
- 2 x GOL: GLYCEROL(Non-functional Binders)
GOL.5: 6 residues within 4Å:- Chain A: T.361, F.364, N.365, A.387, E.391
- Chain D: K.368
6 PLIP interactions:4 interactions with chain A, 2 interactions with chain D- Hydrogen bonds: A:T.361, A:T.361, A:N.365, A:E.391, D:K.368, D:K.368
GOL.15: 6 residues within 4Å:- Chain B: K.368
- Chain C: T.361, F.364, N.365, A.387, E.391
6 PLIP interactions:2 interactions with chain B, 4 interactions with chain C- Hydrogen bonds: B:K.368, B:K.368, C:T.361, C:T.361, C:N.365, C:E.391
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhong, W. et al., `In crystallo' substrate binding triggers major domain movements and reveals magnesium as a co-activator of Trypanosoma brucei pyruvate kinase. Acta Crystallogr.,Sect.D (2013)
- Release Date
- 2013-09-11
- 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 2.30 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 4 x K: POTASSIUM ION(Non-covalent)
- 4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)
- 4 x FDP: 2,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)
- 2 x GOL: GLYCEROL(Non-functional Binders)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhong, W. et al., `In crystallo' substrate binding triggers major domain movements and reveals magnesium as a co-activator of Trypanosoma brucei pyruvate kinase. Acta Crystallogr.,Sect.D (2013)
- Release Date
- 2013-09-11
- Peptides
- Pyruvate kinase 1: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B