SMTL ID : 3hqn.1

Apo crystal structure of Leishmania mexicana(LmPYK)pyruvate kinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: S.54, T.85, K.86, S.212, K.239, E.241 Ligands: K.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.85, A:S.212, A:K.239, A:E.241 GOL.2: 6 residues within 4Å: Chain A: D.233, T.403, R.425, Q.427, T.428, Q.431 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.233, A:D.233, A:N.402, A:Q.427, A:T.428 Water bridges: A:R.425, A:Q.431 GOL.6: 3 residues within 4Å: Chain B: E.439, S.440, F.464 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.440, B:K.468 Water bridges: B:C.429, B:N.433, B:N.433, B:S.440, B:S.440 GOL.10: 7 residues within 4Å: Chain C: S.54, T.85, K.86, S.212, K.239, E.241 Ligands: K.14 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.85, C:S.212, C:K.239, C:E.241 GOL.11: 6 residues within 4Å: Chain C: D.233, T.403, R.425, Q.427, T.428, Q.431 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.233, C:D.233, C:N.402, C:Q.427, C:T.428 Water bridges: C:R.425, C:Q.431 GOL.15: 3 residues within 4Å: Chain D: E.439, S.440, F.464 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.440, D:K.468 Water bridges: D:C.429, D:N.433, D:N.433, D:S.440, D:S.440

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 8 residues within 4Å: Chain A: S.401, N.402, T.403, R.405, S.406, A.482, D.483, H.484 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.402, A:T.403, A:T.403, A:G.404, A:R.405, A:S.406, A:D.483, A:H.484 Water bridges: A:S.406, A:S.406, A:H.484, A:H.484, A:H.484 Salt bridges: A:H.484 SO4.7: 5 residues within 4Å: Chain B: S.401, N.402, T.403, R.405, S.406 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.401, B:N.402, B:T.403, B:G.404, B:R.405, B:S.406, B:S.406 SO4.12: 8 residues within 4Å: Chain C: S.401, N.402, T.403, R.405, S.406, A.482, D.483, H.484 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:N.402, C:T.403, C:T.403, C:G.404, C:R.405, C:S.406, C:D.483, C:H.484 Water bridges: C:S.406, C:S.406, C:H.484, C:H.484, C:H.484 Salt bridges: C:H.484 SO4.16: 5 residues within 4Å: Chain D: S.401, N.402, T.403, R.405, S.406 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.401, D:N.402, D:T.403, D:G.404, D:R.405, D:S.406, D:S.406

8 x K: POTASSIUM ION(Non-covalent)

K.4: 4 residues within 4Å: Chain A: Q.355, S.356, L.358, E.360 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Q.355, A:L.358, A:E.360, H2O.15 K.5: 6 residues within 4Å: Chain A: N.52, S.54, D.84, T.85, K.239 Ligands: GOL.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.54, A:D.84, A:T.85 K.8: 4 residues within 4Å: Chain B: Q.355, S.356, L.358, E.360 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:Q.355, B:L.358, B:E.360, H2O.23, H2O.27 K.9: 6 residues within 4Å: Chain B: N.52, S.54, D.84, T.85, S.212, K.239 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.54, B:D.84, B:T.85, H2O.22 K.13: 4 residues within 4Å: Chain C: Q.355, S.356, L.358, E.360 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:Q.355, C:L.358, C:E.360, H2O.43 K.14: 6 residues within 4Å: Chain C: N.52, S.54, D.84, T.85, K.239 Ligands: GOL.10 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.54, C:D.84, C:T.85 K.17: 4 residues within 4Å: Chain D: Q.355, S.356, L.358, E.360 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:Q.355, D:L.358, D:E.360, H2O.51, H2O.55 K.18: 6 residues within 4Å: Chain D: N.52, S.54, D.84, T.85, S.212, K.239 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.54, D:D.84, D:T.85, H2O.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morgan, H.P. et al., The allosteric mechanism of pryuvate kinase from Leishmania mexicana: a rock and lock model. J.Biol.Chem. (2010)

Release Date

2010-02-16

Peptides

Pyruvate kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
D

D
A

Pyruvate kinase

Related Entries With Identical Sequence