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- PDB-8egf: Branched chain ketoacid dehydrogenase kinase in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 8egf
TitleBranched chain ketoacid dehydrogenase kinase in complex with inhibitor
Components[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Branched-chain ketoacid dehydrogenase / Branched-chain ketoacid dehydrogenase kinase / inhibitors / angiotensin receptor blocker / complex / SIGNALING PROTEIN / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity / Branched-chain amino acid catabolism / : / valine catabolic process / isoleucine catabolic process / pyruvate dehydrogenase (acetyl-transferring) kinase activity / L-leucine catabolic process / branched-chain amino acid catabolic process / lipid biosynthetic process ...[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity / Branched-chain amino acid catabolism / : / valine catabolic process / isoleucine catabolic process / pyruvate dehydrogenase (acetyl-transferring) kinase activity / L-leucine catabolic process / branched-chain amino acid catabolic process / lipid biosynthetic process / protein serine/threonine phosphatase activity / regulation of glucose metabolic process / spermatogenesis / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / mitochondrion / ATP binding
Similarity search - Function
Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal / Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain superfamily / PDK/BCKDK protein kinase / Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / Chem-WIK / Branched-chain alpha-ketoacid dehydrogenase kinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLiu, S.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural studies identify angiotensin II receptor blocker-like compounds as branched-chain ketoacid dehydrogenase kinase inhibitors.
Authors: Liu, S. / Kormos, B.L. / Knafels, J.D. / Sahasrabudhe, P.V. / Rosado, A. / Sommese, R.F. / Reyes, A.R. / Ward, J. / Roth Flach, R.J. / Wang, X. / Buzon, L.M. / Reese, M.R. / Bhattacharya, S. ...Authors: Liu, S. / Kormos, B.L. / Knafels, J.D. / Sahasrabudhe, P.V. / Rosado, A. / Sommese, R.F. / Reyes, A.R. / Ward, J. / Roth Flach, R.J. / Wang, X. / Buzon, L.M. / Reese, M.R. / Bhattacharya, S.K. / Omoto, K. / Filipski, K.J.
History
DepositionSep 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4898
Polymers44,2621
Non-polymers1,2277
Water1,56787
1
A: [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
hetero molecules

A: [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,97716
Polymers88,5232
Non-polymers2,45414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_765-x+2,-y+1,z1
Buried area5100 Å2
ΔGint-86 kcal/mol
Surface area30280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.401, 111.401, 140.547
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-119-

ALA

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Components

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Protein , 1 types, 1 molecules A

#1: Protein [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial / Branched-chain alpha-ketoacid dehydrogenase kinase / BCKD-kinase / BCKDHKIN


Mass: 44261.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Bckdk / Production host: Escherichia coli (BL21 DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3
References: UniProt: Q00972, [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase

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Non-polymers , 5 types, 94 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-WIK / (5P)-5-(4'-methyl[1,1'-biphenyl]-2-yl)-1H-tetrazole


Mass: 236.272 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25 mM ADP against a grid of 100 mM bis-tris pH 5.6-6.5, 1 M lithium sulfate, and 400-840 mM ammonium sulfate
PH range: 5.6-6.5 / Temp details: 20 C

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→96.48 Å / Num. obs: 36703 / % possible obs: 82.5 % / Redundancy: 18.8 % / Biso Wilson estimate: 44.62 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.013 / Net I/σ(I): 28
Reflection shellResolution: 1.85→1.984 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.283 / Num. unique obs: 1836 / CC1/2: 0.714 / Rpim(I) all: 0.538 / % possible all: 74

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 40 / Resolution: 1.85→20.49 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.149 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.138
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1892 5.16 %RANDOM
Rwork0.221 ---
obs0.223 36650 82.5 %-
Displacement parametersBiso max: 174.85 Å2 / Biso mean: 57.69 Å2 / Biso min: 26.29 Å2
Baniso -1Baniso -2Baniso -3
1-2.5191 Å20 Å20 Å2
2--2.5191 Å20 Å2
3----5.0382 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: final / Resolution: 1.85→20.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2599 0 79 87 2765
Biso mean--58.25 44.82 -
Num. residues----325
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1003SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes549HARMONIC5
X-RAY DIFFRACTIONt_it2892HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion366SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3274SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2892HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3941HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion18.51
LS refinement shellResolution: 1.85→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2866 9 5.45 %
Rwork0.2131 156 -
all0.2178 165 -
obs--4.72 %
Refinement TLS params.Method: refined / Origin x: 101.5889 Å / Origin y: 35.7668 Å / Origin z: 22.2433 Å
111213212223313233
T-0.2209 Å20.0596 Å2-0.0102 Å2--0.0162 Å20.0147 Å2---0.2547 Å2
L0.4991 °2-0.0846 °20.5922 °2-0.5459 °2-1.0051 °2--2.8657 °2
S0.1408 Å °0.0636 Å °-0.0009 Å °-0.0366 Å °-0.262 Å °-0.0853 Å °0.3033 Å °0.6539 Å °0.1212 Å °
Refinement TLS groupSelection details: { A|* }

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