SMTL ID : 4h7q.1

Crystal structure of branched-chain alpha-ketoacid dehydrogenase kinase in complex with alpha-ketoisocaproic acid and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 20 residues within 4Å: Chain A: N.279, A.280, R.282, A.283, D.315, G.319, I.320, V.328, F.333, T.334, T.335, G.365, G.367, F.368, G.369, L.370, P.371, T.394 Ligands: MG.3, K.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:N.279, A:R.282, A:D.315, A:T.334, A:T.334, A:T.335, A:T.335, A:G.365, A:G.367, A:G.367, A:G.369, A:L.370 Water bridges: A:D.315, A:F.368, A:F.368, A:T.394, A:T.394 ADP.5: 20 residues within 4Å: Chain B: N.279, A.280, R.282, A.283, D.315, G.319, I.320, V.328, F.333, T.334, T.335, G.365, G.367, F.368, G.369, L.370, P.371, T.394 Ligands: MG.7, K.8 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:N.279, B:R.282, B:D.315, B:T.334, B:T.334, B:T.335, B:T.335, B:G.365, B:G.367, B:G.367, B:G.369, B:L.370, B:T.394 Water bridges: B:D.315, B:F.368, B:F.368

2 x COI: 2-OXO-4-METHYLPENTANOIC ACID(Non-covalent)

COI.2: 6 residues within 4Å: Chain A: I.102, Y.129, H.162, R.197, I.200, R.201 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.102, A:I.200 Salt bridges: A:H.162, A:R.197, A:R.201 COI.6: 6 residues within 4Å: Chain B: I.102, Y.129, H.162, R.197, I.200, R.201 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.102, B:I.200 Hydrogen bonds: B:Y.129 Salt bridges: B:H.162, B:R.197, B:R.201

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.275, N.279 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: E.275, N.279 Ligands: ADP.5 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-covalent)

K.4: 6 residues within 4Å: Chain A: V.328, D.330, F.333, G.367, P.371 Ligands: ADP.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:V.328, A:D.330, A:F.333, A:G.367 K.8: 6 residues within 4Å: Chain B: V.328, D.330, F.333, G.367, P.371 Ligands: ADP.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:V.328, B:D.330, B:F.333, B:G.367

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tso, S.C. et al., Structure-based design and mechanisms of allosteric inhibitors for mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-06-05

Peptides

[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial

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