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- PDB-7pa2: PARK7 with inhibitor 8RK64 -

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Basic information

Entry
Database: PDB / ID: 7pa2
TitlePARK7 with inhibitor 8RK64
ComponentsParkinson disease protein 7
KeywordsUNKNOWN FUNCTION / inhibitor / deglycase
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 / guanine deglycation, glyoxal removal / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / detection of oxidative stress / glyoxal metabolic process / guanine deglycation / positive regulation of NAD(P)H oxidase activity / glycolate biosynthetic process / detoxification of mercury ion / protein deglycase / methylglyoxal metabolic process / positive regulation of mitochondrial electron transport, NADH to ubiquinone / mercury ion binding / protein deglycase activity / 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 / oxidoreductase activity, acting on peroxide as acceptor / lactate biosynthetic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular detoxification of aldehyde / positive regulation of superoxide dismutase activity / small protein activating enzyme 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 transcription regulatory region DNA binding / positive regulation of androgen receptor activity / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / protein deglycosylation / membrane hyperpolarization / negative regulation of protein sumoylation / 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 / ubiquitin-like protein conjugating enzyme binding / insulin secretion / 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 / hydrogen peroxide metabolic process / ubiquitin-specific protease binding / cytokine binding / cuprous ion binding / membrane depolarization / single fertilization / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of neuron apoptotic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / negative regulation of protein ubiquitination / activation of protein kinase B activity / mitochondrion organization / adult locomotory behavior / SUMOylation of transcription cofactors / negative regulation of protein phosphorylation / regulation of mitochondrial membrane potential / negative regulation of protein binding / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / adherens junction / Late endosomal microautophagy / negative regulation of protein kinase activity / positive regulation of protein-containing complex assembly / mitochondrial intermembrane space / PML body / autophagy / kinase binding
Similarity search - Function
Protein/nucleic acid deglycase DJ-1 / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
Chem-6SI / Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsKim, R.Q. / Jia, Y. / Sapmaz, A. / Geurink, P.P.
CitationJournal: J.Med.Chem. / Year: 2022
Title: Chemical Toolkit for PARK7: Potent, Selective, and High-Throughput.
Authors: Jia, Y. / Kim, R.Q. / Kooij, R. / Ovaa, H. / Sapmaz, A. / Geurink, P.P.
History
DepositionJul 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Parkinson disease protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4962
Polymers20,1281
Non-polymers3671
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8790 Å2
Unit cell
Length a, b, c (Å)66.859, 66.859, 179.688
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11AAA-417-

HOH

21AAA-465-

HOH

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Components

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


Mass: 20128.270 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 BL21(DE3) (bacteria) / Variant (production host): Rosetta2
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-6SI / (3~{S})-~{N}-[5-[2-[(azanylidene-$l^{4}-azanylidene)amino]ethanoyl]-6,7-dihydro-4~{H}-[1,3]thiazolo[5,4-c]pyridin-2-yl]-1-(iminomethyl)pyrrolidine-3-carboxamide


Mass: 367.450 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H23N8O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M Bicine pH 9.0 10% (w/v) PEG 20 000 2% (w/v) 1,4-dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96871 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96871 Å / Relative weight: 1
ReflectionResolution: 1.21→59.9 Å / Num. obs: 73359 / % possible obs: 100 % / Redundancy: 18.1 % / CC1/2: 0.999 / Rpim(I) all: 0.028 / Net I/σ(I): 16.1
Reflection shellResolution: 1.21→1.23 Å / Redundancy: 9.6 % / Num. unique obs: 3558 / CC1/2: 0.447 / Rpim(I) all: 0.969 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M8Z

6m8z


Resolution: 1.21→57.902 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.044 / SU ML: 0.02 / Cross valid method: FREE R-VALUE / ESU R: 0.027 / ESU R Free: 0.029
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1547 3631 4.961 %
Rwork0.1324 69558 -
all0.133 --
obs-73189 99.934 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.332 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.175 Å2-0 Å2
2---0.35 Å2-0 Å2
3---1.135 Å2
Refinement stepCycle: LAST / Resolution: 1.21→57.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1384 0 25 168 1577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0131429
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171431
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.6381930
X-RAY DIFFRACTIONr_angle_other_deg1.6121.6023308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3115187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29223.50957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54215254
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg14.049151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.675157
X-RAY DIFFRACTIONr_chiral_restr0.1220.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021637
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02269
X-RAY DIFFRACTIONr_nbd_refined0.2210.2294
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.21341
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2724
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2778
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2340.211
X-RAY DIFFRACTIONr_nbd_other0.1630.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.5290.212
X-RAY DIFFRACTIONr_mcbond_it3.3781.626751
X-RAY DIFFRACTIONr_mcbond_other3.2311.616750
X-RAY DIFFRACTIONr_mcangle_it4.3162.441938
X-RAY DIFFRACTIONr_mcangle_other4.2912.443938
X-RAY DIFFRACTIONr_scbond_it7.2992.201678
X-RAY DIFFRACTIONr_scbond_other7.3382.21679
X-RAY DIFFRACTIONr_scangle_it8.1493.058992
X-RAY DIFFRACTIONr_scangle_other8.1933.068993
X-RAY DIFFRACTIONr_lrange_it6.12222.1131568
X-RAY DIFFRACTIONr_lrange_other6.41521.451527
X-RAY DIFFRACTIONr_rigid_bond_restr6.79432860
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.21-1.2410.2882540.26650440.26753060.8370.85799.84920.256
1.241-1.2750.2372540.22349080.22451670.9080.91499.90320.206
1.275-1.3120.2412520.20348150.20550770.9150.93199.8030.184
1.312-1.3530.1752430.16246270.16248720.9530.95799.9590.138
1.353-1.3970.1712630.14245050.14447710.9570.96399.93710.119
1.397-1.4460.1732200.12743810.1346040.9530.9799.93480.106
1.446-1.5010.1412090.10342480.10544630.9740.9899.86560.085
1.501-1.5620.1122180.08940710.0942930.9830.98599.90680.074
1.562-1.6310.1142250.08639150.08741410.9830.98799.97590.073
1.631-1.7110.1361770.08837880.0939660.9790.98599.97480.077
1.711-1.8030.1242000.08535690.08737690.9810.9881000.075
1.803-1.9130.131860.09834000.135880.980.98599.94430.088
1.913-2.0440.1441640.11932070.1233720.9770.98199.97030.11
2.044-2.2080.141580.11330090.11431680.9820.98599.96840.107
2.208-2.4180.1431290.11228020.11429320.980.98399.96590.108
2.418-2.7030.1351440.11625220.11726660.980.9831000.114
2.703-3.120.1391180.14122660.14123840.9790.9761000.141
3.12-3.8190.2021030.15819500.1620530.9660.9731000.163
3.819-5.3890.138640.14315740.14316380.9840.9821000.151
5.389-57.9020.193500.1899570.18910070.9760.9661000.193

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