+Open data
-Basic information
Entry | Database: PDB / ID: 8pq0 | ||||||
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Title | Structure of human PARK7 in complex with GK16R | ||||||
Components | Parkinson disease protein 7 | ||||||
Keywords | HYDROLASE / Parkinson disease protein 7 / cyanopyrrolidine / DJ-1 | ||||||
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, methylglyoxal removal / : / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate ...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, methylglyoxal removal / : / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal 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 protein K48-linked deubiquitination / negative regulation of ubiquitin-specific protease activity / protein deglycation, glyoxal removal / glycolate biosynthetic process / guanine deglycation, glyoxal removal / glyoxal metabolic process / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / detection of oxidative stress / guanine deglycation / positive regulation of NAD(P)H oxidase activity / detoxification of mercury ion / protein deglycase / methylglyoxal metabolic process / positive regulation of mitochondrial electron transport, NADH to ubiquinone / mercury ion binding / hydrogen peroxide metabolic process / protein deglycase activity / positive regulation of dopamine biosynthetic process / oxidoreductase activity, acting on peroxide as acceptor / superoxide dismutase copper chaperone activity / positive regulation of autophagy of mitochondrion / positive regulation of acute inflammatory response to antigenic stimulus / positive regulation of superoxide dismutase activity / lactate biosynthetic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular detoxification of aldehyde / protein deglycosylation / small protein activating enzyme binding / positive regulation of transcription regulatory region DNA binding / Hydrolases; Acting on ester bonds; Thioester hydrolases / peroxiredoxin activity / 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 / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of protein sumoylation / positive regulation of androgen receptor activity / membrane hyperpolarization / negative regulation of protein export from nucleus / regulation of androgen receptor signaling pathway / cupric ion binding / oxygen sensor activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / insulin secretion / ubiquitin-like protein conjugating enzyme binding / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / positive regulation of reactive oxygen species biosynthetic process / nuclear androgen receptor binding / dopamine uptake involved in synaptic transmission / ubiquitin-specific protease binding / cuprous ion binding / cytokine binding / membrane depolarization / single fertilization / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of neuron apoptotic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / activation of protein kinase B activity / adult locomotory behavior / SUMOylation of transcription cofactors / negative regulation of protein phosphorylation / regulation of mitochondrial membrane potential / mitochondrion organization / negative regulation of protein binding / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / adherens junction / kinase binding / negative regulation of protein kinase activity / positive regulation of DNA-binding transcription factor activity / Late endosomal microautophagy / positive regulation of protein-containing complex assembly / PML body / mitochondrial intermembrane space Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Grethe, C. / Gersch, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2024 Title: N-Cyanopiperazines as Specific Covalent Inhibitors of the Deubiquitinating Enzyme UCHL1. Authors: Schmidt, M. / Grethe, C. / Recknagel, S. / Kipka, G.M. / Klink, N. / Gersch, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pq0.cif.gz | 99.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pq0.ent.gz | 66.6 KB | Display | PDB format |
PDBx/mmJSON format | 8pq0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/8pq0 ftp://data.pdbj.org/pub/pdb/validation_reports/pq/8pq0 | HTTPS FTP |
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-Related structure data
Related structure data | 8ppwC 8pw1C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20071.217 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARK7 / Production host: Escherichia coli (E. coli) 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 |
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#2: Chemical | ChemComp-8RX / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 18.6% (v/v) PEG3350, 170 mM NaNO3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 22, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→33.36 Å / Num. obs: 72940 / % possible obs: 99.4 % / Redundancy: 9.6 % / Biso Wilson estimate: 26.77 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.026 / Rrim(I) all: 0.028 / Net I/σ(I): 35.3 |
Reflection shell | Resolution: 1.48→1.53 Å / Rmerge(I) obs: 0.912 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3838 / CC1/2: 0.808 / Rrim(I) all: 0.963 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→33.36 Å / SU ML: 0.1959 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.726 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→33.36 Å
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Refine LS restraints |
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LS refinement shell |
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