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- PDB-7zpe: human branched Chain Keto Acid Dehydrogenase Kinase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7zpe
Titlehuman branched Chain Keto Acid Dehydrogenase Kinase in complex with ligand
ComponentsBranched-chain alpha-ketoacid dehydrogenase kinase
KeywordsTRANSFERASE / histidine kinase allosteric inhibitor branched chain ketoacid metabolism
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 ketoacid dehydrogenase kinase deficiency / pyruvate dehydrogenase (acetyl-transferring) kinase activity / L-valine catabolic process / regulation of pyruvate decarboxylation to acetyl-CoA / L-isoleucine catabolic process / L-leucine catabolic process / oxoglutarate dehydrogenase complex / amino acid catabolic process ...[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity / Branched-chain ketoacid dehydrogenase kinase deficiency / pyruvate dehydrogenase (acetyl-transferring) kinase activity / L-valine catabolic process / regulation of pyruvate decarboxylation to acetyl-CoA / L-isoleucine catabolic process / L-leucine catabolic process / oxoglutarate dehydrogenase complex / amino acid catabolic process / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / lipid biosynthetic process / protein serine/threonine phosphatase activity / regulation of glucose metabolic process / kinase activity / spermatogenesis / non-specific serine/threonine protein kinase / mitochondrial matrix / 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 superfamily
Similarity search - Domain/homology
: / Branched-chain alpha-ketoacid dehydrogenase kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsKack, H. / Wissler, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Combining druggability, co-evolution and rigidity analysis to map functional pockets
Authors: La Sala, G. / Kack, H. / Pfleger, C. / Nevin, P. / De vivo, M. / Hogner, A. / Tyrchan, C. / Gohlke, H. / Wissler, L. / Frolov, A. / Bohm, K. / Janet, J.-P.
History
DepositionApr 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Branched-chain alpha-ketoacid dehydrogenase kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8807
Polymers44,2521
Non-polymers6286
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint15 kcal/mol
Surface area15120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.594, 129.594, 73.215
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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


Mass: 44251.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCKDK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O14874, non-specific serine/threonine protein kinase, [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-JP6 / 2-[(4-chlorophenyl)methylamino]-5-propyl-6~{H}-[1,2,4]triazolo[1,5-a]pyrimidin-7-one


Mass: 317.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16ClN5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.47 Å3/Da / Density % sol: 64.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 mM Hepes pH 7.5, 0.8 M NaCl, 250 mM KCl, 300 mM arginine,and 1 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2021
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.64→91.7 Å / Num. obs: 17091 / % possible obs: 90.4 % / Redundancy: 11.5 % / CC1/2: 0.99 / Net I/σ(I): 19.8
Reflection shellResolution: 2.64→2.76 Å / Redundancy: 12.6 % / Num. unique obs: 855 / CC1/2: 0.885 / % possible all: 57.2

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (26-JUL-2023)refinement
autoPROC1.1.7data reduction
autoPROC1.1.7data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 40 / Resolution: 2.64→91.64 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.895 / SU R Cruickshank DPI: 0.364 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.362 / SU Rfree Blow DPI: 0.263 / SU Rfree Cruickshank DPI: 0.267
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 852 4.99 %RANDOM
Rwork0.2227 ---
obs0.2244 17091 90.4 %-
Displacement parametersBiso mean: 99.65 Å2
Baniso -1Baniso -2Baniso -3
1--4.3699 Å20 Å20 Å2
2---4.3699 Å20 Å2
3---8.7399 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.64→91.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 0 42 15 2526
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0072563HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.853456HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d909SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes434HARMONIC5
X-RAY DIFFRACTIONt_it2563HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion19.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion325SEMIHARMONIC5
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_contact1901SEMIHARMONIC4
LS refinement shellResolution: 2.64→2.72 Å / Total num. of bins used: 43
RfactorNum. reflection% reflection
Rfree0.4136 -6.14 %
Rwork0.3177 382 -
all0.3241 407 -
obs--25.14 %
Refinement TLS params.Method: refined / Origin x: 160.47 Å / Origin y: 133.422 Å / Origin z: 10.283 Å
111213212223313233
T-0.2616 Å2-0.0524 Å2-0.1562 Å2--0.3824 Å20.0014 Å2---0.1993 Å2
L1.1275 °2-0.2384 °20.1432 °2-4.3737 °2-1.5005 °2--0 °2
S0.0176 Å °0.2954 Å °-0.2113 Å °0.137 Å °-0.0535 Å °-0.4097 Å °0.1677 Å °0.1342 Å °0.0359 Å °
Refinement TLS groupSelection details: { A|* }

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