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- PDB-2q8i: Pyruvate dehydrogenase kinase isoform 3 in complex with antitumor... -

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Basic information

Entry
Database: PDB / ID: 2q8i
TitlePyruvate dehydrogenase kinase isoform 3 in complex with antitumor drug radicicol
Components
  • Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
  • [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3
KeywordsTRANSFERASE / GHKL ATPase/kinase family / pyruvate dehydrogenase complex / mitochondrial kinase / radicicol
Function / homology
Function and homology information


hypoxia-inducible factor-1alpha signaling pathway / PDH complex synthesizes acetyl-CoA from PYR / [pyruvate dehydrogenase (acetyl-transferring)] kinase / pyruvate dehydrogenase (acetyl-transferring) kinase activity / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / regulation of pyruvate decarboxylation to acetyl-CoA / Regulation of pyruvate dehydrogenase (PDH) complex / pyruvate catabolic process / Protein lipoylation ...hypoxia-inducible factor-1alpha signaling pathway / PDH complex synthesizes acetyl-CoA from PYR / [pyruvate dehydrogenase (acetyl-transferring)] kinase / pyruvate dehydrogenase (acetyl-transferring) kinase activity / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / regulation of pyruvate decarboxylation to acetyl-CoA / Regulation of pyruvate dehydrogenase (PDH) complex / pyruvate catabolic process / Protein lipoylation / pyruvate decarboxylation to acetyl-CoA / pyruvate dehydrogenase complex / cellular response to fatty acid / Signaling by Retinoic Acid / regulation of reactive oxygen species metabolic process / regulation of glucose metabolic process / tricarboxylic acid cycle / peroxisome proliferator activated receptor signaling pathway / cellular response to glucose stimulus / peptidyl-serine phosphorylation / glucose metabolic process / protein kinase activity / mitochondrial matrix / protein serine/threonine kinase activity / nucleolus / mitochondrion / ATP binding / identical protein binding
Similarity search - Function
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / 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 / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. ...Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / 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 / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Chloramphenicol acetyltransferase-like domain superfamily / 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 superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Up-down Bundle / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / RADICICOL / DIHYDROLIPOIC ACID / Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial / [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 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: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
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_ref_seq_dif / 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_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_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.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3
B: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1876
Polymers62,4832
Non-polymers7044
Water1,45981
1
A: [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3
B: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
hetero molecules

A: [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3
B: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,37512
Polymers124,9664
Non-polymers1,4098
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z+1/21
Unit cell
Length a, b, c (Å)120.872, 120.872, 239.637
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe second part of the biological assembly is generated by the following operation, Y-X,Y,1/2-Z, of both the chain a and b.

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3 / Pyruvate dehydrogenase kinase isoform 3


Mass: 48290.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDK3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl21
References: UniProt: Q15120, [pyruvate dehydrogenase (acetyl-transferring)] kinase
#2: Protein Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Pyruvate dehydrogenase complex E2 subunit / PDCE2 / E2 / Dihydrolipoamide S-acetyltransferase ...Pyruvate dehydrogenase complex E2 subunit / PDCE2 / E2 / Dihydrolipoamide S-acetyltransferase component of pyruvate dehydrogenase complex / PDC-E2 / 70 kDa mitochondrial autoantigen of primary biliary cirrhosis / PBC / M2 antigen complex 70 kDa subunit


Mass: 14192.097 Da / Num. of mol.: 1 / Fragment: lipoyl-bearing domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLAT, DLTA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P10515, dihydrolipoyllysine-residue acetyltransferase

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Non-polymers , 5 types, 85 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-RDC / RADICICOL / MONORDEN


Mass: 364.777 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17ClO6
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-RED / DIHYDROLIPOIC ACID


Mass: 208.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O2S2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 4.04 Å3/Da / Density % sol: 69.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: soudium citrate, sodium potassium phosphate, sodium chrolide, 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 / Date: Oct 26, 2006 / 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: 2.6→50 Å / Num. obs: 32612 / % possible obs: 100 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.054 / Χ2: 0.836 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.647.10.69415970.7281100
2.64-2.697.70.53915900.7411100
2.69-2.747.80.45215990.7871100
2.74-2.880.37715760.7821100
2.8-2.867.90.32816000.7781100
2.86-2.937.90.25115940.7911100
2.93-37.90.20616010.8131100
3-3.087.90.16916120.7851100
3.08-3.177.80.14216030.7731100
3.17-3.287.90.10316080.7581100
3.28-3.397.80.07816030.791100
3.39-3.537.80.06616280.8371100
3.53-3.697.70.05816110.8691100
3.69-3.887.70.05116350.9661100
3.88-4.137.80.04816220.978199.9
4.13-4.457.60.04516461.115199.9
4.45-4.897.60.03916520.97199.9
4.89-5.67.30.03316760.929199.9
5.6-7.057.40.02917130.8091100
7.05-506.90.02118460.709199.6

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Processing

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

2q8f


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / SU B: 12.535 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1647 5.1 %RANDOM
Rwork0.205 ---
obs0.206 32534 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.257 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.03 Å20 Å2
2--0.05 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3727 0 43 81 3851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223875
X-RAY DIFFRACTIONr_angle_refined_deg1.821.9915250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6715460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81724.078179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.58915665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9131523
X-RAY DIFFRACTIONr_chiral_restr0.1240.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022944
X-RAY DIFFRACTIONr_nbd_refined0.2340.21598
X-RAY DIFFRACTIONr_nbtor_refined0.3230.22611
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2149
X-RAY DIFFRACTIONr_metal_ion_refined0.1930.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.222
X-RAY DIFFRACTIONr_mcbond_it0.8971.52321
X-RAY DIFFRACTIONr_mcangle_it1.69323770
X-RAY DIFFRACTIONr_scbond_it2.69631581
X-RAY DIFFRACTIONr_scangle_it4.1934.51477
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 118 -
Rwork0.333 2227 -
obs-2345 99.96 %

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