SMTL ID : 4hyw.1

Pyruvate kinase (PYK) from Trypanosoma brucei in the presence of Magnesium and F26BP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: E.241, D.265 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.265, H2O.6, H2O.6, H2O.6, H2O.9 MG.5: 2 residues within 4Å: Chain B: E.241, D.265 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.265, H2O.16, H2O.16, H2O.19, H2O.20 MG.9: 2 residues within 4Å: Chain C: E.241, D.265 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.265, H2O.29, H2O.29, H2O.29, H2O.32 MG.13: 2 residues within 4Å: Chain D: E.241, D.265 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.265, H2O.38, H2O.39, H2O.42, H2O.42

4 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: N.52, S.54, D.84, T.85, K.239 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.84, A:T.85, 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.14, H2O.14 K.10: 5 residues within 4Å: Chain C: N.52, S.54, D.84, T.85, K.239 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.84, C:T.85, H2O.27 K.14: 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.37, H2O.37

4 x FDP: 2,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)

FDP.3: 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 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.402, A:N.402, A:T.403, A:R.405, A:S.406, A:S.406, A:K.454, A:A.482, A:G.488 Water bridges: A:K.487, A:K.487 Salt bridges: A:K.454, A:R.457 FDP.7: 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 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: 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:G.488, B:Y.489 Water bridges: B:R.457 Salt bridges: B:K.454, B:R.457 FDP.11: 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 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:N.402, C:N.402, C:T.403, C:R.405, C:S.406, C:S.406, C:K.454, C:A.482, C:G.488 Water bridges: C:K.487, C:K.487 Salt bridges: C:K.454, C:R.457 FDP.15: 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 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: 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:G.488, D:Y.489 Water bridges: D:R.457 Salt bridges: D:K.454, D:R.457

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 1 residues within 4Å: Chain A: K.96 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain C: K.96 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain B: T.361, F.364, N.365, A.387 Chain C: K.368 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.365, B:A.387, C:K.368, C:K.368 GOL.16: 5 residues within 4Å: Chain A: K.368 Chain D: T.361, F.364, N.365, A.387 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:N.365, D:A.387, A:K.368, A:K.368

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
B

B
A

C
B

D
A

Pyruvate kinase 1

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