SMTL ID : 4kcv.1

Pyruvate kinase (PYK) from Trypanosoma brucei soaked with 2-oxoglutaric acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 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: AKG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.241, A:D.265, H2O.5 MG.7: 3 residues within 4Å: Chain B: E.241, D.265 Ligands: AKG.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.241, B:D.265, H2O.18, H2O.18 MG.12: 4 residues within 4Å: Chain C: K.239, E.241, D.265 Ligands: AKG.14 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.241, C:D.265, H2O.34 MG.18: 3 residues within 4Å: Chain D: E.241, D.265 Ligands: AKG.20 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.241, D:D.265, H2O.47, H2O.47

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 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.84, A:T.85, H2O.2, H2O.5 K.8: 5 residues within 4Å: Chain B: N.52, S.54, D.84, T.85, S.212 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.54, B:D.84, B:T.85, H2O.15, H2O.15 K.13: 6 residues within 4Å: Chain C: N.52, S.54, D.84, T.85, S.212, K.239 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.84, C:T.85, H2O.30, H2O.34 K.19: 5 residues within 4Å: Chain D: N.52, S.54, D.84, T.85, S.212 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.54, D:D.84, D:T.85, H2O.44, H2O.44

4 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.3: 12 residues within 4Å: Chain A: R.50, K.239, E.241, M.260, A.262, R.263, G.264, D.265, T.297, M.329, S.331 Ligands: MG.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.239, A:G.264, A:D.265, A:D.265, A:T.297, A:S.331, A:S.331 Water bridges: A:R.50, A:T.297 Salt bridges: A:R.50 AKG.9: 12 residues within 4Å: Chain B: R.50, K.239, E.241, M.260, A.262, R.263, G.264, D.265, T.297, M.329, S.331 Ligands: MG.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.239, B:G.264, B:D.265, B:S.331, B:S.331 Water bridges: B:R.50, B:R.50, B:N.52, B:N.52 Salt bridges: B:R.50 AKG.14: 12 residues within 4Å: Chain C: R.50, K.239, E.241, M.260, A.262, R.263, G.264, D.265, T.297, M.329, S.331 Ligands: MG.12 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:K.239, C:G.264, C:D.265, C:D.265, C:T.297, C:S.331, C:S.331 Water bridges: C:R.50, C:T.297 Salt bridges: C:R.50 AKG.20: 12 residues within 4Å: Chain D: R.50, K.239, E.241, M.260, A.262, R.263, G.264, D.265, T.297, M.329, S.331 Ligands: MG.18 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:K.239, D:G.264, D:D.265, D:S.331, D:S.331 Water bridges: D:R.50, D:R.50, D:N.52, D:N.52 Salt bridges: D:R.50

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 14 PLIP interactions: 14 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:R.405, A:K.487, A:K.487 Salt bridges: A:K.454, A:R.457 FDP.10: 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:R.405, B:S.406, B:S.406, B:K.454, B:A.482, B:V.486, B:G.488, B:Y.489 Water bridges: B:K.454, B:R.457, B:R.457 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 14 PLIP interactions: 14 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:R.405, C:K.487, C:K.487 Salt bridges: C:K.454, C:R.457 FDP.21: 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:R.405, D:S.406, D:S.406, D:K.454, D:A.482, D:V.486, D:G.488, D:Y.489 Water bridges: D:K.454, D:R.457, D:R.457 Salt bridges: D:K.454, D:R.457

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: Q.393, A.394, N.416, C.417 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.416 Water bridges: A:Q.393, A:N.416 GOL.6: 7 residues within 4Å: Chain A: R.23, C.429, L.432, N.433, V.438, V.439, S.440 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.23, A:S.440 Water bridges: A:R.23 GOL.11: 7 residues within 4Å: Chain B: P.88, I.178, N.179, L.180, V.185, R.215, E.269 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:P.88, B:L.180, B:R.215 Water bridges: B:E.269, B:E.269 GOL.16: 4 residues within 4Å: Chain C: Q.393, A.394, N.416, C.417 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.416 Water bridges: C:Q.393, C:N.416 GOL.17: 7 residues within 4Å: Chain C: R.23, C.429, L.432, N.433, V.438, V.439, S.440 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.23, C:S.440 Water bridges: C:R.23 GOL.22: 7 residues within 4Å: Chain D: P.88, I.178, N.179, L.180, V.185, R.215, E.269 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:P.88, D:L.180, D:R.215 Water bridges: D:E.269, D:E.269

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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