SMTL ID : 3qv6.1

Crystal structure of Leishmania mexicana pyruvate kinase(LmPYK)in complex with acid blue 80.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-tetramer

Ligands

4 x QV6: 3-({4-[(2,4-dimethyl-5-sulfophenyl)amino]-9,10-dioxo-9,10-dihydroanthracen-1-yl}amino)-2,4,6-trimethylbenzenesulfonic acid(Non-functional Binders)(Non-covalent)

QV6.1: 1 residues within 4Å: Ligands: QV6.2 No protein-ligand interaction detected (PLIP) QV6.2: 13 residues within 4Å: Chain A: T.27, P.30, R.50, N.52, H.55, G.56, Y.60, Y.305, S.331, G.332, A.335, K.336 Ligands: QV6.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.27, A:P.30, A:A.335, A:K.336, A:K.336 Hydrogen bonds: A:N.52, A:Y.305, A:S.331 Salt bridges: A:R.50, A:K.336 pi-Stacking: A:Y.60 QV6.9: 1 residues within 4Å: Ligands: QV6.10 No protein-ligand interaction detected (PLIP) QV6.10: 13 residues within 4Å: Chain C: T.27, P.30, R.50, N.52, H.55, G.56, Y.60, Y.305, S.331, G.332, A.335, K.336 Ligands: QV6.9 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:T.27, C:P.30, C:A.335, C:K.336, C:K.336 Hydrogen bonds: C:N.52, C:S.331 Salt bridges: C:R.50, C:K.336 pi-Stacking: C:Y.60

8 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: N.52, S.54, D.84, T.85, S.212, K.239 No protein-ligand interaction detected (PLIP) K.4: 4 residues within 4Å: Chain A: Q.355, S.356, L.358, E.360 No protein-ligand interaction detected (PLIP) K.6: 6 residues within 4Å: Chain B: N.52, S.54, D.84, T.85, S.212, K.239 No protein-ligand interaction detected (PLIP) K.7: 4 residues within 4Å: Chain B: Q.355, S.356, L.358, E.360 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Q.355, B:L.358, H2O.5 K.11: 6 residues within 4Å: Chain C: N.52, S.54, D.84, T.85, S.212, K.239 No protein-ligand interaction detected (PLIP) K.12: 4 residues within 4Å: Chain C: Q.355, S.356, L.358, E.360 No protein-ligand interaction detected (PLIP) K.14: 6 residues within 4Å: Chain D: N.52, S.54, D.84, T.85, S.212, K.239 No protein-ligand interaction detected (PLIP) K.15: 4 residues within 4Å: Chain D: Q.355, S.356, L.358, E.360 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:Q.355, D:L.358, H2O.9

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 9 residues within 4Å: Chain A: L.400, S.401, N.402, T.403, G.404, R.405, S.406, A.482, D.483 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:L.400, A:N.402, A:T.403, A:T.403, A:T.403, A:G.404, A:R.405, A:S.406, A:S.406 PO4.8: 9 residues within 4Å: Chain B: L.400, S.401, N.402, T.403, G.404, R.405, S.406, A.482, D.483 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:L.400, B:S.401, B:N.402, B:T.403, B:T.403, B:T.403, B:G.404, B:R.405, B:S.406 PO4.13: 9 residues within 4Å: Chain C: L.400, S.401, N.402, T.403, G.404, R.405, S.406, A.482, D.483 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:L.400, C:N.402, C:T.403, C:T.403, C:T.403, C:G.404, C:R.405, C:S.406, C:S.406, C:D.483 PO4.16: 9 residues within 4Å: Chain D: L.400, S.401, N.402, T.403, G.404, R.405, S.406, A.482, D.483 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:L.400, D:S.401, D:N.402, D:T.403, D:T.403, D:G.404, D:R.405, D:S.406 Water bridges: D:T.403, D:T.403

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morgan, H.P. et al., The trypanocidal drug suramin and other trypan blue mimetics are inhibitors of pyruvate kinases and bind to the adenosine site. J.Biol.Chem. (2011)

Release Date

2011-06-29

Peptides

Pyruvate kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
A

D
D

Pyruvate kinase

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