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- PDB-6lio: Crystal structure of human PDK2 complexed with GM67520 -

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Basic information

Entry
Database: PDB / ID: 6lio
TitleCrystal structure of human PDK2 complexed with GM67520
Components[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
KeywordsTRANSFERASE / mitochondria / kinase / inhibitor
Function / homology
Function and homology information


[pyruvate dehydrogenase (acetyl-transferring)] kinase / regulation of acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase (acetyl-transferring) kinase activity / Regulation of pyruvate dehydrogenase (PDH) complex / regulation of ketone metabolic process / pyruvate dehydrogenase complex / regulation of pH / cellular response to nutrient / Signaling by Retinoic Acid / regulation of gluconeogenesis ...[pyruvate dehydrogenase (acetyl-transferring)] kinase / regulation of acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase (acetyl-transferring) kinase activity / Regulation of pyruvate dehydrogenase (PDH) complex / regulation of ketone metabolic process / pyruvate dehydrogenase complex / regulation of pH / cellular response to nutrient / Signaling by Retinoic Acid / regulation of gluconeogenesis / intrinsic apoptotic signaling pathway by p53 class mediator / regulation of glucose metabolic process / regulation of calcium-mediated signaling / cellular response to reactive oxygen species / glucose metabolic process / insulin receptor signaling pathway / glucose homeostasis / protein kinase activity / mitochondrial matrix / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytosol
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 / 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
Chem-EH3 / [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsKang, J. / Kim, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2016R1D1A1B03930716 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structural basis for the inhibition of PDK2 by novel ATP- and lipoyl-binding site targeting compounds.
Authors: Kang, J. / Pagire, H.S. / Kang, D. / Song, Y.H. / Lee, I.K. / Lee, K.T. / Park, C.J. / Ahn, J.H. / Kim, J.
History
DepositionDec 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
B: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,62811
Polymers92,6712
Non-polymers1,9579
Water8,125451
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-65 kcal/mol
Surface area31640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.949, 95.122, 162.503
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 14 - 381 / Label seq-ID: 39 - 406

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial / Pyruvate dehydrogenase kinase 2 / Pyruvate dehydrogenase kinase isoform 2 / PDKII


Mass: 46335.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDK2, PDHK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q15119, [pyruvate dehydrogenase (acetyl-transferring)] kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EH3 / 4-[[[5-[5-chloranyl-2,4-bis(oxidanyl)phenyl]-4-[4-(1-methylsulfonylpiperidin-4-yl)oxyphenyl]-1,2-oxazol-3-yl]carbonylamino]methyl]cyclohexane-1-carboxylic acid


Mass: 648.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H34ClN3O9S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium sulfate, 0.1M Bis-Tris pH 6.5, 25% Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 86058 / % possible obs: 97.4 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.037 / Rrim(I) all: 0.101 / Χ2: 2.204 / Net I/σ(I): 8 / Num. measured all: 647193
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.76-1.796.41.73443690.550.7361.8891.37499.8
1.79-1.827.71.8243300.6830.6931.9491.415100
1.82-1.8682.11743610.7890.7912.2621.47100
1.86-1.97.643820.9741.657100
1.9-1.946.10.25542870.9740.1170.2823.69999.4
1.94-1.987.844140.9381.79100
1.98-2.038.10.55243680.9380.2060.591.766100
2.03-2.098.10.45443570.9490.1690.4851.828100
2.09-2.158.10.36843640.9640.1370.3931.843100
2.15-2.227.80.57844110.9680.220.6192.073100
2.22-2.34.50.28531860.9790.1460.3232.73472.8
2.3-2.3980.24744090.9870.0930.2642.102100
2.39-2.58.10.16943850.990.0630.182.123100
2.5-2.638.10.13844180.9930.0520.1482.214100
2.63-2.7980.10844290.9950.040.1152.333100
2.79-3.0180.08744480.9960.0330.0932.384100
3.01-3.317.90.07344500.9970.0270.0782.711100
3.31-3.796.80.06334990.9970.0250.0683.12177.8
3.79-4.787.40.05245040.9980.020.0563.24599.6
4.78-5070.05446870.9960.0220.0583.16298.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MP2

4mp2


Resolution: 1.76→36.53 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.637 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2688 4055 5 %RANDOM
Rwork0.2343 ---
obs0.236 76621 91.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.26 Å2 / Biso mean: 34.766 Å2 / Biso min: 20.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--1.31 Å2-0 Å2
3----1.32 Å2
Refinement stepCycle: final / Resolution: 1.76→36.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5769 0 126 451 6346
Biso mean--45.45 44.42 -
Num. residues----725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136093
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175534
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.6428274
X-RAY DIFFRACTIONr_angle_other_deg1.4091.5712867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3775733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.53422.265309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.511151018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7811534
X-RAY DIFFRACTIONr_chiral_restr0.0830.2777
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026732
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021274
Refine LS restraints NCS

Ens-ID: 1 / Number: 11296 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.76→1.806 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 303 -
Rwork0.299 6079 -
all-6382 -
obs--99.07 %

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