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Yorodumi- PDB-6ghk: Human PARP1 (ARTD1) - Catalytic domain in complex with inhibitor ... -
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-Basic information
Entry | Database: PDB / ID: 6ghk | ||||||
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Title | Human PARP1 (ARTD1) - Catalytic domain in complex with inhibitor ME0527 | ||||||
Components | Poly [ADP-ribose] polymerase 1 | ||||||
Keywords | TRANSFERASE / Inhibitor / ADP-ribosyl transferase / Protein-ligand 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 / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Karlberg, T. / Thorsell, A.G. / Lindgren, A.E.G. / Moche, M. / Brock, J. / Ekblad, T. / Spjut, S. / Elofsson, M. / Schuler, H. | ||||||
Citation | Journal: To Be Published Title: Human PARP1 (ARTD1) - Catalytic domain in complex with inhibitor ME0527 Authors: Karlberg, T. / Thorsell, A.G. / Lindgren, A.E.G. / Ekblad, T. / Spjut, S. / Elofsson, M. / Schuler, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ghk.cif.gz | 297.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ghk.ent.gz | 241.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ghk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ghk_validation.pdf.gz | 910.1 KB | Display | wwPDB validaton report |
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Full document | 6ghk_full_validation.pdf.gz | 917.3 KB | Display | |
Data in XML | 6ghk_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 6ghk_validation.cif.gz | 40 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/6ghk ftp://data.pdbj.org/pub/pdb/validation_reports/gh/6ghk | HTTPS FTP |
-Related structure data
Related structure data | 4gv7S S: Starting model for refinement |
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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: 40199.949 Da / Num. of mol.: 2 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: Chemical | ChemComp-SO4 / #4: 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: 2.73 Å3/Da / Density % sol: 54.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 22.5% PEG 3350, 0.18M ammonium sulfate, 0.09M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: May 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→48.85 Å / Num. obs: 39741 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.28→2.42 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.838 / Num. unique obs: 6334 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4gv7 Resolution: 2.28→48.85 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.21
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→48.85 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 20.2579 Å / Origin y: -6.2411 Å / Origin z: 20.1888 Å
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Refinement TLS group | Selection details: all |