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- PDB-6afd: DJ-1 with compound 6 -

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Basic information

Entry
Database: PDB / ID: 6afd
TitleDJ-1 with compound 6
ComponentsProtein/nucleic acid deglycase DJ-1
KeywordsHYDROLASE / DJ-1 / Parkinson's disease / Drug discovery / Fragment-based drug discovery
Function / homology
Function and homology information


tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / peptidyl-cysteine deglycation / peptidyl-arginine deglycation / peptidyl-lysine deglycation / protein deglycation, glyoxal removal / protein deglycation, methylglyoxal removal / : / detoxification of hydrogen peroxide ...tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / peptidyl-cysteine deglycation / peptidyl-arginine deglycation / peptidyl-lysine deglycation / protein deglycation, glyoxal removal / protein deglycation, methylglyoxal removal / : / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal removal / guanine deglycation, glyoxal removal / cellular detoxification of methylglyoxal / regulation of supramolecular fiber organization / negative regulation of death-inducing signaling complex assembly / negative regulation of TRAIL-activated apoptotic signaling pathway / positive regulation of pyrroline-5-carboxylate reductase activity / positive regulation of tyrosine 3-monooxygenase activity / positive regulation of L-dopa biosynthetic process / positive regulation of L-dopa decarboxylase activity / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / glyoxalase (glycolic acid-forming) activity / negative regulation of ubiquitin-specific protease activity / negative regulation of protein K48-linked deubiquitination / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / positive regulation of NAD(P)H oxidase activity / glycolate biosynthetic process / detection of oxidative stress / glyoxal metabolic process / guanine deglycation / detoxification of mercury ion / protein deglycase / methylglyoxal metabolic process / positive regulation of mitochondrial electron transport, NADH to ubiquinone / mercury ion binding / protein deglycase activity / oxidoreductase activity, acting on peroxide as acceptor / positive regulation of dopamine biosynthetic process / positive regulation of autophagy of mitochondrion / superoxide dismutase copper chaperone activity / positive regulation of acute inflammatory response to antigenic stimulus / positive regulation of superoxide dismutase activity / lactate biosynthetic process / : / cellular detoxification of aldehyde / positive regulation of transcription regulatory region DNA binding / protein deglycosylation / small protein activating enzyme binding / peroxiredoxin activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of ubiquitin-protein transferase activity / detoxification of copper ion / negative regulation of protein acetylation / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of androgen receptor activity / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of protein sumoylation / membrane hyperpolarization / negative regulation of protein export from nucleus / regulation of androgen receptor signaling pathway / cupric ion binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / insulin secretion / ubiquitin-like protein conjugating enzyme binding / oxygen sensor activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / hydrogen peroxide metabolic process / nuclear androgen receptor binding / positive regulation of reactive oxygen species biosynthetic process / dopamine uptake involved in synaptic transmission / ubiquitin-specific protease binding / cytokine binding / cuprous ion binding / membrane depolarization / single fertilization / regulation of neuron apoptotic process / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / activation of protein kinase B activity / negative regulation of protein phosphorylation / SUMOylation of transcription cofactors / adult locomotory behavior / regulation of mitochondrial membrane potential / negative regulation of protein binding / positive regulation of interleukin-8 production / mitochondrion organization / negative regulation of extrinsic apoptotic signaling pathway / adherens junction / positive regulation of DNA-binding transcription factor activity / negative regulation of protein kinase activity / positive regulation of protein-containing complex assembly / Late endosomal microautophagy / kinase binding / PML body / mitochondrial intermembrane space
Similarity search - Function
Protein/nucleic acid deglycase DJ-1 / : / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
7-methyl-1~{H}-indole-2,3-dione / Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsCaaveiro, J.M.M. / Tashiro, S. / Tsumoto, K.
Funding support Japan, 4items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)Platform for Drug Discovery, Informatics and Structural Life Science Japan
Japan Society for the Promotion of Science25249115 Japan
Japan Society for the Promotion of Science16H02420 Japan
Japan Society for the Promotion of Science15K06962 Japan
Citation
Journal: ACS Chem. Biol. / Year: 2018
Title: Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
Authors: Tashiro, S. / Caaveiro, J.M.M. / Nakakido, M. / Tanabe, A. / Nagatoishi, S. / Tamura, Y. / Matsuda, N. / Liu, D. / Hoang, Q.Q. / Tsumoto, K.
#1: Journal: Biochemistry / Year: 2014
Title: Thermodynamic and structural characterization of the specific binding of Zn(II) to human protein DJ-1.
Authors: Tashiro, S. / Caaveiro, J.M.M. / Wu, C.X. / Hoang, Q.Q. / Tsumoto, K.
History
DepositionAug 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein/nucleic acid deglycase DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2754
Polymers19,9171
Non-polymers3583
Water4,414245
1
A: Protein/nucleic acid deglycase DJ-1
hetero molecules

A: Protein/nucleic acid deglycase DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5508
Polymers39,8342
Non-polymers7166
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area3100 Å2
ΔGint-35 kcal/mol
Surface area14640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.390, 75.390, 75.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Protein/nucleic acid deglycase DJ-1 / Maillard deglycase / Oncogene DJ1 / Parkinson disease protein 7 / Parkinsonism-associated deglycase ...Maillard deglycase / Oncogene DJ1 / Parkinson disease protein 7 / Parkinsonism-associated deglycase / Protein DJ-1 / DJ-1


Mass: 19917.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK7 / Plasmid: pET28B / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q99497, Hydrolases; Acting on ester bonds; Thioester hydrolases, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, protein deglycase
#2: Chemical ChemComp-72S / 7-methyl-1~{H}-indole-2,3-dione


Mass: 161.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7NO2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsThere are two reaction forms of 72S in this structure. 72S(201) is bonded with Cys106 through a ...There are two reaction forms of 72S in this structure. 72S(201) is bonded with Cys106 through a double bond opening, and 72S(202) is bonded to Lys148 through Schiff base.

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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: 3.1 Å3/Da / Density % sol: 60.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM TRIS-HCl, 200mM sodium citrate, 30% PEG-400, 5mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→32.6 Å / Num. obs: 41594 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.1
Reflection shellResolution: 1.48→1.56 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.766 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLM7.0.9data reduction
SCALA3.3.21data scaling
PHASER2.5.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SOA

1soa


Resolution: 1.48→32.6 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.754 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.044 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14344 1300 3.1 %RANDOM
Rwork0.11892 ---
obs0.11967 40258 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.981 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.03 Å20 Å2
2--0.05 Å20 Å2
3----0.16 Å2
Refinement stepCycle: 1 / Resolution: 1.48→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1376 0 24 245 1645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191447
X-RAY DIFFRACTIONr_bond_other_d0.0010.021474
X-RAY DIFFRACTIONr_angle_refined_deg1.6622.0181957
X-RAY DIFFRACTIONr_angle_other_deg0.8793.0043409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3835194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94325.30649
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05915267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.776157
X-RAY DIFFRACTIONr_chiral_restr0.1090.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211617
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02276
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6551.394755
X-RAY DIFFRACTIONr_mcbond_other1.5511.388754
X-RAY DIFFRACTIONr_mcangle_it2.0352.094944
X-RAY DIFFRACTIONr_mcangle_other2.082.098945
X-RAY DIFFRACTIONr_scbond_it3.1671.795692
X-RAY DIFFRACTIONr_scbond_other3.1651.795693
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5422.5151009
X-RAY DIFFRACTIONr_long_range_B_refined4.31514.1011837
X-RAY DIFFRACTIONr_long_range_B_other3.48712.5031687
X-RAY DIFFRACTIONr_rigid_bond_restr3.96632920
X-RAY DIFFRACTIONr_sphericity_free32.298569
X-RAY DIFFRACTIONr_sphericity_bonded10.32353078
LS refinement shellResolution: 1.481→1.519 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 94 -
Rwork0.247 2930 -
obs--100 %

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