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- PDB-8f4q: rat branched chain ketoacid dehydrogenase kinase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8f4q
Titlerat branched chain ketoacid dehydrogenase kinase in complex with inhibtors
Components[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
KeywordsSIGNALING PROTEIN / TRANSFERASE/INHIBITOR / branched chain ketoacid dehydrogenase kinase / inhibitor / 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 / L-leucine catabolic process / valine catabolic process / isoleucine catabolic process / pyruvate dehydrogenase (acetyl-transferring) kinase activity / 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 / L-leucine catabolic process / valine catabolic process / isoleucine catabolic process / pyruvate dehydrogenase (acetyl-transferring) kinase activity / 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-XER / Branched-chain alpha-ketoacid dehydrogenase kinase
Similarity search - Component
Biological speciesRattus (rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 Å
AuthorsLiu, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Discovery of branched-chain ketoacid dehydrogenase kinase (BDK) inhibitors acting as stabilizers or destabilizers
Authors: Roth Flach, R. / Filipski, K. / Bollinger, E.
History
DepositionNov 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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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)45,5917
Polymers44,2621
Non-polymers1,3296
Water1,15364
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)91,18214
Polymers88,5232
Non-polymers2,65912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_765-x+2,-y+1,z1
Buried area4360 Å2
ΔGint-72 kcal/mol
Surface area29480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.67, 111.67, 139.34
Angle α, β, γ (deg.)90, 90, 120
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-555-

HOH

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Components

#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 (rat) / Gene: Bckdk / Production host: Escherichia coli (E. coli)
References: UniProt: Q00972, [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-XER / 3-chloro-5-fluorothieno[3,2-b]thiophene-2-carboxylic acid


Mass: 236.671 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H2ClFO2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
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: 2.83 Å3/Da / Density % sol: 56.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 5.4, 0.2 M magnesium chloride, and 10% PEG-3350

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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 R 4M / Detector: PIXEL / Date: Oct 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→92.7 Å / Num. obs: 22708 / % possible obs: 88 % / Redundancy: 18.6 % / CC1/2: 1 / Rpim(I) all: 0.017 / Net I/σ(I): 22.6
Reflection shellResolution: 2.154→2.305 Å / Num. unique obs: 1136 / CC1/2: 0.602 / Rpim(I) all: 0.611

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 4 / Resolution: 2.151→23.66 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.257 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.262 / SU Rfree Blow DPI: 0.216 / SU Rfree Cruickshank DPI: 0.215
RfactorNum. reflection% reflectionSelection details
Rfree0.2705 1176 -RANDOM
Rwork0.2336 ---
obs0.2355 22679 79.7 %-
Displacement parametersBiso mean: 80.02 Å2
Baniso -1Baniso -2Baniso -3
1-1.0981 Å20 Å20 Å2
2--1.0981 Å20 Å2
3----2.1961 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.151→23.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2560 0 76 64 2700
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082697HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.853664HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d939SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes498HARMONIC5
X-RAY DIFFRACTIONt_it2694HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion345SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1967SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion17.24
LS refinement shellResolution: 2.151→2.27 Å
RfactorNum. reflection% reflection
Rfree0.3065 27 -
Rwork0.3003 --
obs--11.1 %
Refinement TLS params.Origin x: 101.7881 Å / Origin y: 36.0858 Å / Origin z: 22.7462 Å
111213212223313233
T-0.1425 Å20.06 Å20.0242 Å2-0.0724 Å2-0.0139 Å2---0.1249 Å2
L0.487 °2-0.0584 °20.7804 °2-0.7069 °2-1.0268 °2--3.3608 °2
S0.1644 Å °-0.0935 Å °0.3445 Å °-0.0935 Å °-0.2529 Å °0.7148 Å °0.3445 Å °0.7148 Å °0.0885 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A25 - 374
2X-RAY DIFFRACTION1{ A|* }A401 - 701

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