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- PDB-6lin: Crystal structure of human PDK2 complexed with GM10030 -

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Basic information

Entry
Database: PDB / ID: 6lin
TitleCrystal structure of human PDK2 complexed with GM10030
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 / : / pyruvate dehydrogenase complex / regulation of cellular ketone metabolic process / regulation of pH / cellular response to nutrient / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid ...[pyruvate dehydrogenase (acetyl-transferring)] kinase / regulation of acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase (acetyl-transferring) kinase activity / : / pyruvate dehydrogenase complex / regulation of cellular ketone metabolic process / regulation of pH / cellular response to nutrient / Regulation of pyruvate dehydrogenase (PDH) complex / 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 / phosphorylation / 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-EH0 / DI(HYDROXYETHYL)ETHER / [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsKang, J. / Kim, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, 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
C: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
D: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,14512
Polymers185,3434
Non-polymers2,8028
Water2,702150
1
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)94,1617
Polymers92,6712
Non-polymers1,4905
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-40 kcal/mol
Surface area32980 Å2
MethodPISA
2
C: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
D: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9835
Polymers92,6712
Non-polymers1,3123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-11 kcal/mol
Surface area32840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.420, 156.186, 102.012
Angle α, β, γ (deg.)90.000, 103.970, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUTHRTHRAA13 - 38438 - 409
21LEULEUTHRTHRBB13 - 38438 - 409
12ASPASPTHRTHRAA4 - 38429 - 409
22ASPASPTHRTHRCC4 - 38429 - 409
13LEULEUHISHISAA13 - 38138 - 406
23LEULEUHISHISDD13 - 38138 - 406
14LEULEUGLNGLNBB13 - 38338 - 408
24LEULEUGLNGLNCC13 - 38338 - 408
15LEULEUTYRTYRBB13 - 38238 - 407
25LEULEUTYRTYRDD13 - 38238 - 407
16LEULEUHISHISCC13 - 38138 - 406
26LEULEUHISHISDD13 - 38138 - 406

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#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.: 4
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

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Non-polymers , 5 types, 158 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical
ChemComp-EH0 / 4-[[[4-[3,5-bis(fluoranyl)-4-(4-oxidanyl-4-oxidanylidene-butoxy)phenyl]-5-[5-chloranyl-2,4-bis(oxidanyl)phenyl]-1,2-oxazol-3-yl]carbonylamino]methyl]benzoic acid


Mass: 602.924 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C28H21ClF2N2O9 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium sulfate monohydrate, 0.1M Bis-Tris pH 6.5, 25% w/v 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: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.67→50 Å / Num. obs: 49194 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.104 / Rrim(I) all: 0.245 / Χ2: 1.851 / Net I/σ(I): 4.7 / Num. measured all: 259808
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.67-2.725.21.39924700.4120.6541.5482.33299.7
2.72-2.775.31.70624280.6280.7971.8881.5699.8
2.77-2.825.21.35724590.6730.6391.5041.52199.9
2.82-2.885.31.11824560.780.5231.2381.55899.8
2.88-2.945.31.00724520.7870.4711.1141.59699.9
2.94-3.015.30.89324600.8140.4170.9891.59499.9
3.01-3.085.40.78424360.8640.3630.8671.58699.9
3.08-3.175.30.62224740.8690.290.6881.635100
3.17-3.265.40.48324170.9120.2240.5341.681100
3.26-3.365.40.40624860.9460.1880.4491.666100
3.36-3.485.20.33324560.9510.1560.3692.21599.9
3.48-3.625.40.29624520.970.1380.3271.825100
3.62-3.795.20.22124950.9750.1040.2452.436100
3.79-3.995.20.17524330.9820.0840.1952.437100
3.99-4.245.40.13424320.990.0630.1491.83599.8
4.24-4.565.30.09924690.9930.0470.111.984100
4.56-5.025.40.08724750.9950.0410.0971.842100
5.02-5.755.40.09224910.9940.0430.1011.69299.9
5.75-7.245.30.09824820.9930.0460.1081.7499.9
7.24-5050.06224710.9960.0310.072.3698.3

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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: 2.67→39.08 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.887 / SU B: 17.655 / SU ML: 0.355 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2797 2442 5 %RANDOM
Rwork0.2232 ---
obs0.2261 46026 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 142.03 Å2 / Biso mean: 48.125 Å2 / Biso min: 17.01 Å2
Baniso -1Baniso -2Baniso -3
1-3.65 Å20 Å22.11 Å2
2---0.78 Å20 Å2
3----3.48 Å2
Refinement stepCycle: final / Resolution: 2.67→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11286 0 191 150 11627
Biso mean--62.45 37.73 -
Num. residues----1448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01311763
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710522
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.66115986
X-RAY DIFFRACTIONr_angle_other_deg1.2411.5724377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17951442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.07522.402562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.525151895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5571560
X-RAY DIFFRACTIONr_chiral_restr0.0680.21521
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022408
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A107180.11
12B107180.11
21A109340.09
22C109340.09
31A106330.11
32D106330.11
41B107540.1
42C107540.1
51B112050.07
52D112050.07
61C106990.1
62D106990.1
LS refinement shellResolution: 2.67→2.739 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 163 -
Rwork0.321 3392 -
all-3555 -
obs--99.69 %

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