SMTL ID : 3tz5.1

Crystal structure of branched-chain alpha-ketoacid dehydrogenase kinase/phenylbutyrate complex with ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 22 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, H.364, G.365, F.366, G.367, F.368, G.369, L.370, P.371, T.394 Ligands: MG.2, K.3 19 PLIP interactions: 19 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:H.364, A:H.364, A:F.366, A:G.367, A:G.367, A:G.369, A:L.370 Water bridges: A:R.282, A:D.315, A:F.368, A:F.368, A:T.394 ADP.5: 22 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, H.364, G.365, F.366, G.367, F.368, G.369, L.370, P.371, T.394 Ligands: MG.6, K.7 19 PLIP interactions: 19 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:H.364, B:F.366, B:G.367, B:G.367, B:G.369, B:L.370, B:T.394 Water bridges: B:R.282, B:D.315, B:H.364, B:F.368, B:F.368

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.275, N.279 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.6: 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.3: 6 residues within 4Å: Chain A: V.328, D.330, F.333, G.367, P.371 Ligands: ADP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:V.328, A:D.330, A:F.333 K.7: 6 residues within 4Å: Chain B: V.328, D.330, F.333, G.367, P.371 Ligands: ADP.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:V.328, B:D.330, B:F.333

2 x CLT: 4-PHENYL-BUTANOIC ACID(Non-covalent)

CLT.4: 12 residues within 4Å: Chain A: L.98, I.102, Y.129, L.136, L.158, L.159, H.162, V.165, R.197, I.200, R.201, A.204 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.98, A:I.102, A:Y.129, A:L.136, A:L.158, A:L.158, A:L.159, A:H.162, A:R.197, A:I.200, A:A.204 Hydrogen bonds: A:Y.129 Salt bridges: A:H.162, A:R.197, A:R.201 CLT.8: 12 residues within 4Å: Chain B: L.98, I.102, Y.129, L.136, L.158, L.159, H.162, V.165, R.197, I.200, R.201, A.204 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.98, B:I.102, B:Y.129, B:L.136, B:L.158, B:L.158, B:L.159, B:H.162, B:R.197, B:I.200, B:A.204 Salt bridges: B:H.162, B:R.197, B:R.201

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

2012-10-03

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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