SMTL ID : 1y8p.1

Crystal structure of the PDK3-L2 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.63 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.260, N.264 Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: E.260, N.264 Ligands: ATP.9 No protein-ligand interaction detected (PLIP)

4 x K: POTASSIUM ION(Non-covalent)

K.2: 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.3: 6 residues within 4Å: Chain A: L.313, N.315, Y.318, G.338, P.342 Ligands: ATP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:L.313, A:G.338 K.7: 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 K.8: 6 residues within 4Å: Chain C: L.313, N.315, Y.318, G.338, P.342 Ligands: ATP.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:L.313, C:G.338

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 24 residues within 4Å: Chain A: E.260, K.263, N.264, S.265, R.267, A.268, D.300, V.305, L.313, Y.318, S.319, T.320, L.334, A.335, G.336, F.337, G.338, Y.339, G.340, L.341, P.342, T.365 Ligands: MG.1, K.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:E.260, A:N.264, A:R.267, A:R.267, A:D.300, A:S.319, A:T.320, A:T.320, A:G.336, A:F.337, A:G.338, A:Y.339, A:G.340, A:L.341 Water bridges: A:D.300, A:G.302, A:T.365 Salt bridges: A:K.263 ATP.9: 24 residues within 4Å: Chain C: E.260, K.263, N.264, S.265, R.267, A.268, D.300, V.305, L.313, Y.318, S.319, T.320, L.334, A.335, G.336, F.337, G.338, Y.339, G.340, L.341, P.342, T.365 Ligands: MG.6, K.8 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:E.260, C:E.260, C:N.264, C:R.267, C:R.267, C:D.300, C:S.319, C:T.320, C:T.320, C:G.336, C:F.337, C:G.338, C:Y.339, C:G.340, C:L.341, C:T.365 Water bridges: C:D.300, C:G.302 Salt bridges: C:K.263

2 x RED: DIHYDROLIPOIC ACID(Covalent)

RED.5: 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.10: 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., Crystal structure of pyruvate dehydrogenase kinase 3 bound to lipoyl domain 2 of human pyruvate dehydrogenase complex. Embo J. (2005)

Release Date

2005-05-24

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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