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Yorodumi- PDB-5kpp: Structure of human PARP1 catalytic domain bound to a quinazoline-... -
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-Basic information
Entry | Database: PDB / ID: 5kpp | ||||||
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Title | Structure of human PARP1 catalytic domain bound to a quinazoline-2,4(1H,3H)-dione inhibitor | ||||||
Components | Poly [ADP-ribose] polymerase 1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / Complex / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / regulation of base-excision repair / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / carbohydrate biosynthetic process / positive regulation of single strand break repair ...NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / regulation of base-excision repair / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / carbohydrate biosynthetic process / positive regulation of single strand break repair / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis / negative regulation of adipose tissue development / NAD+-protein-serine ADP-ribosyltransferase activity / regulation of catalytic activity / NAD DNA ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / mitochondrial DNA metabolic process / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / signal transduction involved in regulation of gene expression / positive regulation of necroptotic process / ATP generation from poly-ADP-D-ribose / replication fork reversal / transcription regulator activator activity / HDR through MMEJ (alt-NHEJ) / R-SMAD binding / positive regulation of DNA-templated transcription, elongation / positive regulation of intracellular estrogen receptor signaling pathway / NAD+ ADP-ribosyltransferase / cellular response to zinc ion / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / response to aldosterone / mitochondrial DNA repair / positive regulation of mitochondrial depolarization / negative regulation of cGAS/STING signaling pathway / protein poly-ADP-ribosylation / positive regulation of cardiac muscle hypertrophy / negative regulation of transcription elongation by RNA polymerase II / nuclear replication fork / NAD+-protein ADP-ribosyltransferase activity / site of DNA damage / positive regulation of SMAD protein signal transduction / macrophage differentiation / protein autoprocessing / decidualization / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of double-strand break repair via homologous recombination / POLB-Dependent Long Patch Base Excision Repair / nucleosome binding / SUMOylation of DNA damage response and repair proteins / protein localization to chromatin / negative regulation of innate immune response / telomere maintenance / nucleotidyltransferase activity / transforming growth factor beta receptor signaling pathway / cellular response to nerve growth factor stimulus / mitochondrion organization / nuclear estrogen receptor binding / protein-DNA complex / response to gamma radiation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / DNA Damage Recognition in GG-NER / protein modification process / cellular response to insulin stimulus / Dual Incision in GG-NER / histone deacetylase binding / Formation of Incision Complex in GG-NER / positive regulation of protein localization to nucleus / cellular response to amyloid-beta / nuclear envelope / NAD binding / regulation of protein localization / cellular response to UV / double-strand break repair / site of double-strand break / positive regulation of canonical NF-kappaB signal transduction / cellular response to oxidative stress / chromosome, telomeric region / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / damaged DNA binding / nuclear body / DNA repair / innate immune response / negative regulation of DNA-templated transcription / chromatin binding / DNA damage response / ubiquitin protein ligase binding / chromatin / nucleolus / protein kinase binding / apoptotic process / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.33 Å | ||||||
Authors | Cao, R. / Wang, Y.L. / Zhou, J. / Huang, N. / Xu, B.L. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of human PARP1 catalytic domain bound to a quinazoline-2,4(1H,3H)-dione inhibitor Authors: Cao, R. / Wang, Y.L. / Zhou, J. / Huang, N. / Xu, B.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kpp.cif.gz | 152.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kpp.ent.gz | 119.5 KB | Display | PDB format |
PDBx/mmJSON format | 5kpp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kpp_validation.pdf.gz | 998.3 KB | Display | wwPDB validaton report |
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Full document | 5kpp_full_validation.pdf.gz | 1007.4 KB | Display | |
Data in XML | 5kpp_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 5kpp_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/5kpp ftp://data.pdbj.org/pub/pdb/validation_reports/kp/5kpp | HTTPS FTP |
-Related structure data
Related structure data | 5kpnC 5kpoC 5kpqC 5wrqC 5wryC 5wtcC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39168.809 Da / Num. of mol.: 2 / Fragment: catalytic domain, UNP residues 662-1011 / Mutation: V762A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARP1, ADPRT, PPOL / Production host: Escherichia coli (E. coli) / References: UniProt: P09874, NAD+ ADP-ribosyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.5M AMMONIUM SULFATE, 100mM TRIS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→92.66 Å / Num. obs: 32359 / % possible obs: 98.6 % / Redundancy: 11.7 % / Net I/σ(I): 21.7 |
-Processing
Software |
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Refinement | Resolution: 2.33→81.74 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.901 / SU B: 11.436 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R: 0.515 / ESU R Free: 0.296 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.719 Å2
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Refinement step | Cycle: LAST / Resolution: 2.33→81.74 Å
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