SMTL ID : 4kct.1

Pyruvate kinase (PYK) from Trypanosoma brucei soaked with Oxaloacetate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: K.239, E.241, D.265 Ligands: PYR.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.241, A:D.265, H2O.8, H2O.8 MG.6: 3 residues within 4Å: Chain B: E.241, D.265 Ligands: PYR.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.241, B:D.265, H2O.23, H2O.23 MG.12: 4 residues within 4Å: Chain C: K.239, E.241, D.265 Ligands: PYR.14 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.241, C:D.265, H2O.38, H2O.38 MG.17: 3 residues within 4Å: Chain D: E.241, D.265 Ligands: PYR.19 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.241, D:D.265, H2O.53, H2O.53

4 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: N.52, S.54, D.84, T.85, S.212 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.54, A:D.84, A:T.85, H2O.2, H2O.9 K.7: 6 residues within 4Å: Chain B: N.52, S.54, D.84, T.85, S.212, K.239 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.54, B:D.84, B:T.85, H2O.17, H2O.23 K.13: 5 residues within 4Å: Chain C: N.52, S.54, D.84, T.85, S.212 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.54, C:D.84, C:T.85, H2O.32, H2O.39 K.18: 6 residues within 4Å: Chain D: N.52, S.54, D.84, T.85, S.212, K.239 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.54, D:D.84, D:T.85, H2O.47, H2O.53

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.3: 10 residues within 4Å: Chain A: K.239, E.241, M.260, A.262, R.263, G.264, D.265, T.297, M.329 Ligands: MG.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.239, A:G.264, A:D.265, A:T.297 Water bridges: A:R.50 PYR.8: 10 residues within 4Å: Chain B: K.239, E.241, M.260, A.262, R.263, G.264, D.265, T.297, M.329 Ligands: MG.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.262 Hydrogen bonds: B:K.239, B:G.264, B:D.265 Water bridges: B:R.50 Salt bridges: B:K.239 PYR.14: 10 residues within 4Å: Chain C: K.239, E.241, M.260, A.262, R.263, G.264, D.265, T.297, M.329 Ligands: MG.12 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.239, C:G.264, C:D.265, C:T.297 Water bridges: C:R.50 PYR.19: 10 residues within 4Å: Chain D: K.239, E.241, M.260, A.262, R.263, G.264, D.265, T.297, M.329 Ligands: MG.17 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:A.262 Hydrogen bonds: D:K.239, D:G.264, D:D.265 Water bridges: D:R.50 Salt bridges: 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:S.401, 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:V.486, A:G.488, A:Y.489 Water bridges: A:K.454, A:K.454, A:R.457 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 19 PLIP interactions: 19 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 Water bridges: B:R.405, B:R.405, B:R.405, B:R.405, B:K.454, B:R.457 Salt bridges: B:R.405, 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 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:S.401, 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:V.486, C:G.488, C:Y.489 Water bridges: C:K.454, C:K.454, C:R.457 Salt bridges: C:K.454, C:R.457 FDP.20: 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 19 PLIP interactions: 19 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 Water bridges: D:R.405, D:R.405, D:R.405, D:R.405, D:K.454, D:R.457 Salt bridges: D:R.405, D:K.454, D:R.457

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: P.88, I.90, I.178, N.179, L.180, V.185, L.187, F.213, E.269 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.88, A:L.180, A:L.180, A:E.269 Water bridges: A:N.242 GOL.10: 7 residues within 4Å: Chain B: P.88, I.178, N.179, L.180, F.213, R.215, E.269 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.88, B:L.180, B:R.215, B:E.269 GOL.11: 3 residues within 4Å: Chain B: H.55, G.56, Y.60 No protein-ligand interaction detected (PLIP) GOL.16: 9 residues within 4Å: Chain C: P.88, I.90, I.178, N.179, L.180, V.185, L.187, F.213, E.269 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:P.88, C:L.180, C:L.180, C:E.269 Water bridges: C:N.242 GOL.21: 7 residues within 4Å: Chain D: P.88, I.178, N.179, L.180, F.213, R.215, E.269 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:P.88, D:L.180, D:R.215, D:E.269 GOL.22: 3 residues within 4Å: Chain D: H.55, G.56, Y.60 No protein-ligand interaction detected (PLIP)

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
B

B
A

C
B

D
A

Pyruvate kinase 1

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