SMTL ID : 8egd.1

Branched chain ketoacid dehydrogenase kinase in complex with inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 20 residues within 4Å: Chain A: K.248, N.249, R.252, A.253, D.285, G.289, I.290, V.298, F.303, T.304, T.305, F.336, G.337, F.338, G.339, L.340, P.341, T.364 Ligands: MG.2, K.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.249, A:R.252, A:D.285, A:T.304, A:T.304, A:T.305, A:T.305, A:F.336, A:G.337, A:G.339, A:L.340 Water bridges: A:A.250, A:A.253, A:D.285, A:T.364, A:T.364 Salt bridges: A:K.248, A:R.252 ADP.10: 20 residues within 4Å: Chain B: K.248, N.249, R.252, A.253, D.285, G.289, I.290, V.298, F.303, T.304, T.305, F.336, G.337, F.338, G.339, L.340, P.341, T.364 Ligands: MG.11, K.12 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:N.249, B:R.252, B:D.285, B:T.304, B:T.304, B:T.305, B:T.305, B:F.336, B:G.337, B:G.339, B:L.340 Water bridges: B:A.250, B:A.253, B:D.285, B:T.364, B:T.364 Salt bridges: B:K.248, B:R.252

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: E.245, K.248, N.249, G.339 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.245 MG.11: 5 residues within 4Å: Chain B: E.245, K.248, N.249, G.339 Ligands: ADP.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.245

2 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: V.298, D.300, F.303, G.337, P.341 Ligands: ADP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:V.298, A:D.300, A:F.303 K.12: 6 residues within 4Å: Chain B: V.298, D.300, F.303, G.337, P.341 Ligands: ADP.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:V.298, B:D.300, B:F.303

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 7 residues within 4Å: Chain A: S.37, R.39, R.71, H.74, R.75, K.162, S.166 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.37, A:S.166 Water bridges: A:R.39, A:R.39, A:R.71, A:R.71, A:R.75, A:R.75 Salt bridges: A:R.39, A:R.71, A:H.74, A:R.75, A:K.162 SO4.5: 1 residues within 4Å: Chain A: R.171 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.171 SO4.6: 3 residues within 4Å: Chain A: N.225, G.226 Chain B: R.286 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.226 Salt bridges: B:R.286 SO4.13: 7 residues within 4Å: Chain B: S.37, R.39, R.71, H.74, R.75, K.162, S.166 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.37, B:S.166 Water bridges: B:R.39, B:R.39, B:R.71, B:R.71, B:R.75, B:R.75 Salt bridges: B:R.39, B:R.71, B:H.74, B:R.75, B:K.162 SO4.14: 1 residues within 4Å: Chain B: R.171 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.171 SO4.15: 3 residues within 4Å: Chain A: R.286 Chain B: N.225, G.226 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.286 Hydrogen bonds: B:G.226

6 x WIH: 5-(4-methoxyphenyl)-1H-tetrazole(Non-covalent)

WIH.7: 14 residues within 4Å: Chain A: L.40, T.41, P.42, M.45, R.71, G.169, M.172, L.173, H.176, I.190, I.191, I.235, Y.349, F.380 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:M.172, A:L.173, A:F.380 Hydrogen bonds: A:R.71, A:R.71, A:Y.349, A:Y.349 Water bridges: A:R.39, A:F.380 WIH.8: 13 residues within 4Å: Chain A: L.68, I.72, Y.99, L.106, V.125, L.128, L.129, H.132, V.135, R.167, I.170, R.171, A.174 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.72, A:L.128, A:L.129, A:I.170 Hydrogen bonds: A:Y.99, A:Y.99, A:H.132, A:R.167, A:R.171 WIH.9: 11 residues within 4Å: Chain A: L.82, P.83, I.86, I.92, L.139, G.142, L.143, I.150, L.155, V.156, F.159 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.82, A:I.86, A:I.86, A:V.156, A:F.159, A:F.159 WIH.16: 14 residues within 4Å: Chain B: L.40, T.41, P.42, M.45, R.71, G.169, M.172, L.173, H.176, I.190, I.191, I.235, Y.349, F.380 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:M.172, B:L.173, B:F.380 Hydrogen bonds: B:L.40, B:R.71, B:R.71, B:Y.349 Water bridges: B:R.39, B:F.380 WIH.17: 13 residues within 4Å: Chain B: L.68, I.72, Y.99, L.106, V.125, L.128, L.129, H.132, V.135, R.167, I.170, R.171, A.174 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.72, B:L.128, B:L.129, B:I.170 Hydrogen bonds: B:Y.99, B:Y.99, B:H.132, B:R.167, B:R.171 WIH.18: 11 residues within 4Å: Chain B: L.82, P.83, I.86, I.92, L.139, G.142, L.143, I.150, L.155, V.156, F.159 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.82, B:I.86, B:I.86, B:V.156, B:F.159, B:F.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, S. et al., Structural studies identify angiotensin II receptor blocker-like compounds as branched-chain ketoacid dehydrogenase kinase inhibitors. J.Biol.Chem. (2023)

Release Date

2023-03-08

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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