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- PDB-2q8h: Structure of pyruvate dehydrogenase kinase isoform 1 in complex w... -

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Basic information

Entry
Database: PDB / ID: 2q8h
TitleStructure of pyruvate dehydrogenase kinase isoform 1 in complex with dichloroacetate (DCA)
Components[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 1
KeywordsTRANSFERASE / GHKL ATPase/kinase family / pyruvate dehydrogenase complex / mitochondrial kinase / dichroloacetate
Function / homology
Function and homology information


hypoxia-inducible factor-1alpha signaling pathway / [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 / Signaling by Retinoic Acid / intrinsic apoptotic signaling pathway in response to oxidative stress / regulation of glucose metabolic process / glucose metabolic process ...hypoxia-inducible factor-1alpha signaling pathway / [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 / Signaling by Retinoic Acid / intrinsic apoptotic signaling pathway in response to oxidative stress / regulation of glucose metabolic process / glucose metabolic process / cell population proliferation / mitochondrial matrix / protein kinase activity / phosphorylation / mitochondrion / ATP binding
Similarity search - Function
Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain / 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 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 ...Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain / 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 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / DICHLORO-ACETIC ACID / [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsKato, M. / Li, J. / Chuang, J.L. / Chuang, D.T.
CitationJournal: Structure / Year: 2007
Title: Distinct Structural Mechanisms for Inhibition of Pyruvate Dehydrogenase Kinase Isoforms by AZD7545, Dichloroacetate, and Radicicol.
Authors: Kato, M. / Li, J. / Chuang, J.L. / Chuang, D.T.
History
DepositionJun 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5303
Polymers46,3621
Non-polymers1682
Water4,360242
1
A: [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 1
hetero molecules

A: [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0596
Polymers92,7232
Non-polymers3364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5120 Å2
ΔGint-44 kcal/mol
Surface area32330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)98.323, 98.323, 110.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-462-

HOH

DetailsThe second part of the biological assembly is generated by the following operation: Y,X,-Z

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Components

#1: Protein [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 1 / Pyruvate dehydrogenase kinase isoform 1


Mass: 46361.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDK1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q15118, [pyruvate dehydrogenase (acetyl-transferring)] kinase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-TF4 / DICHLORO-ACETIC ACID / Dichloroacetic acid


Mass: 128.942 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H2Cl2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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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: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 293 K / pH: 5.6
Details: 0.42 M NaK tartrate, 0.1 M Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98 Å
DetectorType: SBC-3 / Detector: CCD / Details: mirror
RadiationMonochromator: si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 37074 / % possible obs: 99.4 %
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.561 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 2Q8F

2q8f


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.827 / SU ML: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.277 1802 5 %
Rwork0.23 --
obs0.232 36097 96.8 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 44.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 7 242 3201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223052
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.9634139
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0425364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33223.533150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75515513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5731522
X-RAY DIFFRACTIONr_chiral_restr0.1010.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022347
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.21433
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22076
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2235
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2750.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.821.51836
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47322976
X-RAY DIFFRACTIONr_scbond_it2.17131239
X-RAY DIFFRACTIONr_scangle_it3.1744.51162
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å
RfactorNum. reflection% reflection
Rfree0.441 120 -
Rwork0.372 2495 -
obs--96.07 %

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