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- PDB-3tz4: Crystal structure of branched-chain alpha-ketoacid dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 3tz4
TitleCrystal structure of branched-chain alpha-ketoacid dehydrogenase kinase/S-alpha-chloroisocaproate complex with ADP
Components[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / GHKL protein kinase / Allosteric kinase inhibitor / Branched-chain alpha-ketoacid / Branched-chain amino acids / Maple syrup urine disease / Diabetes and obesity / Bergerat nucleotide-binding fold / Protein kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 amino acid catabolism / L-leucine catabolic process / valine catabolic process / isoleucine catabolic process / : / pyruvate dehydrogenase (acetyl-transferring) kinase activity / branched-chain amino acid catabolic process / regulation of glucose metabolic process ...[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity / Branched-chain amino acid catabolism / L-leucine catabolic process / valine catabolic process / isoleucine catabolic process / : / pyruvate dehydrogenase (acetyl-transferring) kinase activity / branched-chain amino acid catabolic process / regulation of glucose metabolic process / spermatogenesis / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / 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 / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain ...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 / Signal transduction histidine kinase-related protein, C-terminal / 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
(2S)-2-chloro-4-methylpentanoic acid / ADENOSINE-5'-DIPHOSPHATE / : / Branched-chain alpha-ketoacid dehydrogenase kinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsTso, S.C. / Chuang, J.L. / Gui, W.J. / Wynn, R.M. / Li, J. / Chuang, D.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure-based design and mechanisms of allosteric inhibitors for mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase.
Authors: Tso, S.C. / Qi, X. / Gui, W.J. / Chuang, J.L. / Morlock, L.K. / Wallace, A.L. / Ahmed, K. / Laxman, S. / Campeau, P.M. / Lee, B.H. / Hutson, S.M. / Tu, B.P. / Williams, N.S. / Tambar, U.K. / ...Authors: Tso, S.C. / Qi, X. / Gui, W.J. / Chuang, J.L. / Morlock, L.K. / Wallace, A.L. / Ahmed, K. / Laxman, S. / Campeau, P.M. / Lee, B.H. / Hutson, S.M. / Tu, B.P. / Williams, N.S. / Tambar, U.K. / Wynn, R.M. / Chuang, D.T.
History
DepositionSep 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0155
Polymers47,3741
Non-polymers6414
Water1,44180
1
A: [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
hetero molecules

A: [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,03110
Polymers94,7482
Non-polymers1,2828
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area924.3 Å2
2
A: [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
hetero molecules

A: [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,03110
Polymers94,7482
Non-polymers1,2828
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1160 Å2
ΔGint-8 kcal/mol
Surface area30250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.953, 127.953, 73.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsTHE AUTHORS PROVIDED BURIED SURFACE AREA IS 924.3 A2

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 47374.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Bckdk / Plasmid: pTrckHisB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21GroESL
References: UniProt: Q00972, [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase

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Non-polymers , 5 types, 84 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-03H / (2S)-2-chloro-4-methylpentanoic acid / (S)-alpha-chloroisocaproate


Mass: 150.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11ClO2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 3.17 Å3/Da / Density % sol: 61.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14% peg8000, 0.1 M Tris, pH8.5, 1.2 M NaCl, 125mM KCl, 150mM Arg-HCl,20mM MgCl2, 5% glycerol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97864 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2011 / Details: mirrors
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97864 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 29510 / Num. obs: 29447 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Rmerge(I) obs: 0.052 / Rsym value: 0.04
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 8 % / Rmerge(I) obs: 0.932 / Mean I/σ(I) obs: 2.48 / Rsym value: 0.745 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.7.1_743)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.1_743phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→45.129 Å / SU ML: 0.62 / σ(F): 1.89 / Phase error: 22.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 1586 5.05 %random
Rwork0.2016 ---
obs0.2021 29447 99.72 %-
all-31494 --
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.344 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.4857 Å20 Å20 Å2
2---5.4857 Å2-0 Å2
3---10.9715 Å2
Refinement stepCycle: LAST / Resolution: 2.25→45.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 38 80 2614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072608
X-RAY DIFFRACTIONf_angle_d1.1063534
X-RAY DIFFRACTIONf_dihedral_angle_d13.397993
X-RAY DIFFRACTIONf_chiral_restr0.069393
X-RAY DIFFRACTIONf_plane_restr0.004449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.27110.34991570.30122636X-RAY DIFFRACTION99
2.2711-2.35230.23491380.23812662X-RAY DIFFRACTION100
2.3523-2.44640.24081350.21662682X-RAY DIFFRACTION100
2.4464-2.55780.28021560.21782658X-RAY DIFFRACTION100
2.5578-2.69260.24131360.20412679X-RAY DIFFRACTION100
2.6926-2.86130.21391310.20392712X-RAY DIFFRACTION100
2.8613-3.08210.24061330.21072712X-RAY DIFFRACTION100
3.0821-3.39220.23341530.19622696X-RAY DIFFRACTION100
3.3922-3.88280.19791650.18912734X-RAY DIFFRACTION100
3.8828-4.8910.16131490.1742768X-RAY DIFFRACTION100
4.891-45.1380.22831330.21592881X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 3.0601 Å / Origin y: -30.3946 Å / Origin z: 10.059 Å
111213212223313233
T0.3657 Å20.0018 Å20.0067 Å2-0.4217 Å20.0741 Å2--0.3849 Å2
L3.8094 °20.6673 °2-1.1991 °2-2.0939 °2-0.4922 °2--0.811 °2
S-0.0664 Å °-0.4858 Å °-0.2936 Å °0.0027 Å °-0.0348 Å °0.2237 Å °0.0527 Å °0.0814 Å °0.077 Å °
Refinement TLS groupSelection details: all

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