SMTL ID : 2q8i.1

Pyruvate dehydrogenase kinase isoform 3 in complex with antitumor drug radicicol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-2-2-mer

Ligands

2 x K: POTASSIUM ION(Non-covalent)

K.1: 6 residues within 4Å: Chain A: S.33, R.34, F.35, N.72, V.384, F.385 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.33, A:F.35, A:F.385 K.5: 6 residues within 4Å: Chain C: S.33, R.34, F.35, N.72, V.384, F.385 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.33, C:F.35, C:F.385

2 x RDC: RADICICOL(Non-covalent)

RDC.2: 12 residues within 4Å: Chain A: L.261, N.264, S.265, R.267, A.268, D.300, G.304, V.305, L.313, L.341, L.357, T.365 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.264, A:A.268, A:V.305, A:L.313, A:T.365 Hydrogen bonds: A:L.261, A:N.264 Water bridges: A:G.302, A:G.304, A:A.367 RDC.6: 12 residues within 4Å: Chain C: L.261, N.264, S.265, R.267, A.268, D.300, G.304, V.305, L.313, L.341, L.357, T.365 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:N.264, C:A.268, C:V.305, C:L.313, C:T.365 Hydrogen bonds: C:L.261, C:N.264, C:T.365 Water bridges: C:G.302, C:G.304, C:A.367

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: I.310, D.311, F.314, K.356, L.357, Y.358 Chain C: K.356, Y.358 Ligands: GOL.7 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:L.357, A:Y.358, C:K.356, C:K.356 Water bridges: A:R.345 GOL.7: 9 residues within 4Å: Chain A: K.356, Y.358 Chain C: I.310, D.311, F.314, K.356, L.357, Y.358 Ligands: GOL.3 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:L.357, C:Y.358, A:K.356, A:K.356, A:Y.358 Water bridges: C:R.345

2 x RED: DIHYDROLIPOIC ACID(Covalent)

RED.4: 5 residues within 4Å: Chain A: F.48, S.58, F.61 Chain B: K.68 Chain C: R.410 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.48, A:F.61, A:F.61 RED.8: 5 residues within 4Å: Chain A: R.410 Chain C: F.48, S.58, F.61 Chain D: K.68 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.48, C:F.61, C:F.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kato, M. et al., Distinct Structural Mechanisms for Inhibition of Pyruvate Dehydrogenase Kinase Isoforms by AZD7545, Dichloroacetate, and Radicicol. Structure (2007)

Release Date

2007-07-24

Peptides

[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3: AC
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

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