SMTL ID : 3srk.1

A new class of suicide inhibitor blocks nucleotide binding to pyruvate kinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-tetramer

Ligands

4 x LSA: 1,2-BENZISOTHIAZOL-3(2H)-ONE 1,1-DIOXIDE(Covalent)

LSA.1: 7 residues within 4Å: Chain A: I.28, G.29, N.52, H.55, Y.60, A.335, K.336 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.60 Water bridges: A:K.336, A:K.336 LSA.5: 8 residues within 4Å: Chain B: I.28, G.29, N.52, H.55, G.56, Y.60, A.335, K.336 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:H.55, B:Y.60 Hydrogen bonds: B:N.52 LSA.8: 7 residues within 4Å: Chain C: I.28, G.29, N.52, H.55, Y.60, A.335, K.336 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.60 Water bridges: C:K.336, C:K.336 LSA.12: 8 residues within 4Å: Chain D: I.28, G.29, N.52, H.55, G.56, Y.60, A.335, K.336 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:H.55, D:Y.60 Hydrogen bonds: D:N.52

8 x K: POTASSIUM ION(Non-covalent)

K.2: 2 residues within 4Å: Chain A: E.241, D.265 No protein-ligand interaction detected (PLIP) K.3: 3 residues within 4Å: Chain A: Q.355, L.358, E.360 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:Q.355, A:L.358 K.6: 4 residues within 4Å: Chain B: Q.355, S.356, L.358, E.360 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Q.355, B:L.358, B:E.360, H2O.123 K.7: 2 residues within 4Å: Chain B: E.241, D.265 No protein-ligand interaction detected (PLIP) K.9: 2 residues within 4Å: Chain C: E.241, D.265 No protein-ligand interaction detected (PLIP) K.10: 3 residues within 4Å: Chain C: Q.355, L.358, E.360 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:Q.355, C:L.358 K.13: 4 residues within 4Å: Chain D: Q.355, S.356, L.358, E.360 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:Q.355, D:L.358, D:E.360, H2O.260 K.14: 2 residues within 4Å: Chain D: E.241, D.265 No protein-ligand interaction detected (PLIP)

2 x PTK: PYRENE-1,3,6,8-TETRASULFONIC ACID(Non-covalent)

PTK.4: 2 residues within 4Å: Chain A: R.195, K.225 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:R.195, A:R.195, A:K.225 pi-Cation interactions: A:R.195 PTK.11: 2 residues within 4Å: Chain C: R.195, K.225 4 PLIP interactions: 4 interactions with chain C Salt bridges: C:R.195, C:R.195, C:K.225 pi-Cation interactions: C:R.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morgan, H.P. et al., A new class of suicide inhibitor blocks nucleotide binding to pyruvate kinase. To be Published

Release Date

2012-07-18

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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