SMTL ID : 3ktx.1

Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK)in complex with 1,3,6,8-pyrenetetrasulfonic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: S.401, N.402, T.403, R.405, S.406, Y.489 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.402, A:T.403, A:R.405, A:S.406 Water bridges: A:Y.489, A:Y.489 GOL.2: 6 residues within 4Å: Chain A: R.224, R.232, D.233, I.234, M.235, D.257 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.224, A:R.232, A:D.257, A:Q.431 GOL.4: 6 residues within 4Å: Chain A: K.280, F.322, N.323, F.363 Chain B: L.4, N.7 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:N.7, A:N.323 Water bridges: B:L.4, A:K.280, A:K.280, A:S.284, A:F.322 GOL.5: 7 residues within 4Å: Chain A: T.27, R.50, N.52, S.331, G.332, K.336 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.50, A:N.52, A:K.336, A:K.336 GOL.6: 3 residues within 4Å: Chain A: P.30, H.55 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.55 Water bridges: A:K.336, A:K.336 GOL.7: 5 residues within 4Å: Chain B: H.55, S.331, G.332, A.335, K.336 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.50, B:H.55 GOL.8: 6 residues within 4Å: Chain C: S.401, N.402, T.403, R.405, S.406, Y.489 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.402, C:T.403, C:R.405, C:S.406 GOL.9: 6 residues within 4Å: Chain C: R.224, R.232, D.233, I.234, M.235, D.257 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.224, C:R.232, C:D.257, C:Q.431 GOL.11: 6 residues within 4Å: Chain C: K.280, F.322, N.323, F.363 Chain D: L.4, N.7 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.323, D:N.7 Water bridges: C:K.280, C:K.280, C:S.284, C:F.322, D:L.4 GOL.12: 7 residues within 4Å: Chain C: T.27, R.50, N.52, S.331, G.332, K.336 Ligands: GOL.13 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.50, C:N.52, C:K.336, C:K.336 GOL.13: 3 residues within 4Å: Chain C: P.30, H.55 Ligands: GOL.12 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.55, C:H.55 Water bridges: C:K.336, C:K.336 GOL.14: 5 residues within 4Å: Chain D: H.55, S.331, G.332, A.335, K.336 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.55 Water bridges: D:R.50

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

PTK.3: 2 residues within 4Å: Chain A: R.195, K.225 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.195 pi-Cation interactions: A:R.195, A:R.195 PTK.10: 2 residues within 4Å: Chain C: R.195, K.225 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:R.195 pi-Cation interactions: C:R.195, C:R.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morgan, H.P. et al., An improved strategy for the crystallization of Leishmania mexicana pyruvate kinase. Acta Crystallogr.,Sect.F (2010)

Release Date

2010-02-09

Peptides

Pyruvate kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Pyruvate kinase

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