SMTL ID : 8egf.1

Branched chain ketoacid dehydrogenase kinase in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 20 residues within 4Å: Chain A: E.245, K.248, N.249, R.252, A.253, D.285, G.289, I.290, V.298, F.303, T.304, T.305, G.335, F.336, G.337, G.339, L.340, P.341, T.364 Ligands: K.2 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:E.245, A:N.249, A:D.285, A:T.304, A:T.304, A:T.305, A:T.305, A:A.306, A:G.337, A:G.337, A:L.340 Water bridges: A:K.248, A:A.250, A:R.252, A:A.253, A:D.285, A:F.338, A:T.364, A:T.364 Salt bridges: A:K.248, A:R.252 ADP.8: 20 residues within 4Å: Chain B: E.245, K.248, N.249, R.252, A.253, D.285, G.289, I.290, V.298, F.303, T.304, T.305, G.335, F.336, G.337, G.339, L.340, P.341, T.364 Ligands: K.9 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:E.245, B:N.249, B:D.285, B:T.304, B:T.304, B:T.305, B:T.305, B:A.306, B:G.337, B:G.337, B:L.340 Water bridges: B:K.248, B:A.250, B:R.252, B:A.253, B:D.285, B:F.338, B:T.364, B:T.364 Salt bridges: B:K.248, B:R.252

2 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: V.298, D.300, F.303, G.337, P.341 Ligands: ADP.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:V.298, A:D.300, A:F.303, A:G.337 K.9: 6 residues within 4Å: Chain B: V.298, D.300, F.303, G.337, P.341 Ligands: ADP.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:V.298, B:D.300, B:F.303, B:G.337

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

SO4.3: 6 residues within 4Å: Chain A: S.37, R.39, R.71, H.74, K.162, S.166 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.37 Water bridges: A:R.39, 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 SO4.4: 3 residues within 4Å: Chain A: R.286 Chain B: N.225, G.226 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.226, B:G.226 Salt bridges: A:R.286 SO4.7: 2 residues within 4Å: Chain A: R.194, R.231 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.194 SO4.10: 6 residues within 4Å: Chain B: S.37, R.39, R.71, H.74, K.162, S.166 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.37 Water bridges: B:R.39, 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 SO4.11: 3 residues within 4Å: Chain A: N.225, G.226 Chain B: R.286 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.286 Hydrogen bonds: A:G.226, A:G.226 SO4.14: 2 residues within 4Å: Chain B: R.194, R.231 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.194

4 x WIK: (5P)-5-(4'-methyl[1,1'-biphenyl]-2-yl)-1H-tetrazole(Non-covalent)

WIK.5: 15 residues within 4Å: Chain A: R.39, L.40, P.42, M.45, Y.63, R.71, G.169, M.172, L.173, H.176, I.190, I.191, I.235, Y.349, L.350 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:M.172, A:I.235, A:Y.349 Hydrogen bonds: A:R.71, A:R.71, A:Y.349 WIK.6: 12 residues within 4Å: Chain A: I.72, L.128, L.129, H.132, K.133, V.136, R.167, I.170, R.171, G.331, P.332, Y.346 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.129, A:R.167, A:R.171 Hydrogen bonds: A:R.167 Water bridges: A:Y.346, A:Y.346 pi-Cation interactions: A:R.167 WIK.12: 15 residues within 4Å: Chain B: R.39, L.40, P.42, M.45, Y.63, R.71, G.169, M.172, L.173, H.176, I.190, I.191, I.235, Y.349, L.350 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:M.172, B:I.235, B:Y.349 Hydrogen bonds: B:R.71, B:R.71, B:Y.349 WIK.13: 12 residues within 4Å: Chain B: I.72, L.128, L.129, H.132, K.133, V.136, R.167, I.170, R.171, G.331, P.332, Y.346 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.129, B:R.167, B:R.171 Hydrogen bonds: B:R.167 Water bridges: B:Y.346, B:Y.346 pi-Cation interactions: B:R.167

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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