SMTL ID : 3pp7.1

Crystal structure of Leishmania mexicana pyruvate kinase in complex with the drug suramin, an inhibitor of glycolysis.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

2 x PTK: pyrene-1,3,6,8-tetrasulfonic acid(Non-covalent)

PTK.1: 1 residues within 4Å: Chain A: R.194 6 PLIP interactions: 6 interactions with chain A Water bridges: A:A.188 Salt bridges: A:R.194, A:R.194 pi-Cation interactions: A:R.194, A:R.194, A:R.194 PTK.9: 1 residues within 4Å: Chain C: R.194 6 PLIP interactions: 6 interactions with chain C Water bridges: C:A.188 Salt bridges: C:R.194, C:R.194 pi-Cation interactions: C:R.194, C:R.194, C:R.194

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: P.87, E.88, I.89, V.177, N.178, F.212 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:I.89, A:I.89, A:V.177 Water bridges: A:E.88, A:E.240, A:E.240, A:E.268 GOL.8: 5 residues within 4Å: Chain B: K.85, S.211, K.238, E.240, D.264 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.85, B:K.238, B:K.238, B:D.264 GOL.10: 6 residues within 4Å: Chain C: P.87, E.88, I.89, V.177, N.178, F.212 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:I.89, C:I.89, C:V.177 Water bridges: C:E.240, C:E.240, C:E.268 GOL.16: 5 residues within 4Å: Chain D: K.85, S.211, K.238, E.240, D.264 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.85, D:K.238, D:K.238, D:D.264

8 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: Q.354, S.355, L.357, E.359 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Q.354, A:L.357, A:E.359, H2O.5 K.4: 5 residues within 4Å: Chain A: N.51, S.53, D.83, T.84, K.238 No protein-ligand interaction detected (PLIP) K.6: 6 residues within 4Å: Chain B: N.51, S.53, D.83, T.84, S.211, K.238 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.84 K.7: 4 residues within 4Å: Chain B: Q.354, S.355, L.357, E.359 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Q.354, B:L.357, H2O.13 K.11: 4 residues within 4Å: Chain C: Q.354, S.355, L.357, E.359 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:Q.354, C:L.357, C:E.359, H2O.22 K.12: 5 residues within 4Å: Chain C: N.51, S.53, D.83, T.84, K.238 No protein-ligand interaction detected (PLIP) K.14: 6 residues within 4Å: Chain D: N.51, S.53, D.83, T.84, S.211, K.238 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.84 K.15: 4 residues within 4Å: Chain D: Q.354, S.355, L.357, E.359 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:Q.354, D:L.357, H2O.30

2 x SVR: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID(Non-covalent)

SVR.5: 11 residues within 4Å: Chain B: T.26, P.29, R.49, N.51, H.54, G.55, Y.59, S.330, G.331, A.334, K.335 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:P.29, B:P.29, B:A.334 Hydrogen bonds: B:T.26, B:R.49 Water bridges: B:N.51 Salt bridges: B:H.54, B:H.54, B:H.54, B:K.335 pi-Stacking: B:H.54, B:H.54, B:Y.59 SVR.13: 11 residues within 4Å: Chain D: T.26, P.29, R.49, N.51, H.54, G.55, Y.59, S.330, G.331, A.334, K.335 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:P.29, D:P.29, D:A.334 Hydrogen bonds: D:R.49, D:N.51 Salt bridges: D:H.54, D:H.54, D:H.54, D:K.335 pi-Stacking: D:H.54, D:H.54, D:Y.59

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

2010-12-15

Peptides

Pyruvate kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Pyruvate kinase