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- PDB-4dzy: Crystal structure of branched-chain alpha-ketoacid dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 4dzy
TitleCrystal structure of branched-chain alpha-ketoacid dehydrogenase kinase/(S)-2-chloro-3-phenylpropanoic acid 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 / valine catabolic process / L-leucine catabolic process / isoleucine catabolic process / pyruvate dehydrogenase (acetyl-transferring) kinase activity / oxoglutarate dehydrogenase complex / branched-chain amino acid catabolic process / lipid biosynthetic process ...[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity / Branched-chain amino acid catabolism / valine catabolic process / L-leucine catabolic process / isoleucine catabolic process / pyruvate dehydrogenase (acetyl-transferring) kinase activity / oxoglutarate dehydrogenase complex / branched-chain amino acid catabolic process / lipid biosynthetic process / protein serine/threonine phosphatase activity / regulation of glucose metabolic process / phosphorylation / spermatogenesis / non-specific serine/threonine protein kinase / protein kinase activity / mitochondrial matrix / 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
ADENOSINE-5'-DIPHOSPHATE / : / (S)-2-chloro-3-phenylpropanoic acid / Branched-chain alpha-ketoacid dehydrogenase kinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 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
DepositionMar 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: 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 / 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_ref_seq_dif.details / _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

Downloads & links

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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)48,0495
Polymers47,3741
Non-polymers6754
Water1,45981
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)96,09910
Polymers94,7482
Non-polymers1,3508
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Unit cell
Length a, b, c (Å)127.326, 127.326, 73.249
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-540-

HOH

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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, 85 molecules

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


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-WJ1 / (S)-2-chloro-3-phenylpropanoic acid


Mass: 184.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9ClO2
#6: 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.74 %
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: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2011 / Details: mirrors
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 35704 / Num. obs: 35683 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 42.3 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.043 / Net I/σ(I): 31.1
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 2.67 / Num. unique all: 1753 / Rsym value: 0.661 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.refine: 1.7.1_743)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.7.1_743phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.101→44.956 Å / SU ML: 0.57 / σ(F): 1.34 / Phase error: 20.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 2000 5.61 %random
Rwork0.2054 ---
obs0.2068 35633 99.9 %-
all-35669 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5713 Å2-0 Å2-0 Å2
2---2.5713 Å20 Å2
3---5.1427 Å2
Refinement stepCycle: LAST / Resolution: 2.101→44.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2489 0 41 81 2611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082605
X-RAY DIFFRACTIONf_angle_d1.1483529
X-RAY DIFFRACTIONf_dihedral_angle_d14.664991
X-RAY DIFFRACTIONf_chiral_restr0.072390
X-RAY DIFFRACTIONf_plane_restr0.004450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1006-2.15310.26591400.23232355X-RAY DIFFRACTION99
2.1531-2.21130.30751400.22432356X-RAY DIFFRACTION100
2.2113-2.27640.21771400.21382354X-RAY DIFFRACTION100
2.2764-2.34990.25351400.20452367X-RAY DIFFRACTION100
2.3499-2.43390.24141420.20762385X-RAY DIFFRACTION100
2.4339-2.53130.25181420.20152368X-RAY DIFFRACTION100
2.5313-2.64650.23961410.20662375X-RAY DIFFRACTION100
2.6465-2.7860.20941410.20732379X-RAY DIFFRACTION100
2.786-2.96050.29641430.22092399X-RAY DIFFRACTION100
2.9605-3.18910.231430.20992410X-RAY DIFFRACTION100
3.1891-3.50990.24781430.20912408X-RAY DIFFRACTION100
3.5099-4.01750.21551440.20642418X-RAY DIFFRACTION100
4.0175-5.06050.19611470.1762469X-RAY DIFFRACTION100
5.0605-44.96630.23961540.21812590X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 3.2865 Å / Origin y: -30.2046 Å / Origin z: 9.7435 Å
111213212223313233
T0.1906 Å20.0142 Å20.0154 Å2-0.2718 Å20.0465 Å2--0.212 Å2
L0.6952 °20.4014 °2-0.3856 °2-0.5542 °2-0.2574 °2---0.0819 °2
S-0.0384 Å °-0.1716 Å °-0.1072 Å °-0.1099 Å °-0.0191 Å °0.0739 Å °-0.0002 Å °0.0257 Å °0 Å °
Refinement TLS groupSelection details: all

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