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- PDB-8gla: Co-crystal structure of caPCNA bound to the AOH1996 derivative, A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8gla | ||||||
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Title | Co-crystal structure of caPCNA bound to the AOH1996 derivative, AOH1996-1LE | ||||||
![]() | Proliferating cell nuclear antigen | ||||||
![]() | DNA BINDING PROTEIN / PCNA / transcription-replication conflict / DNA replication stress / DNA repair / AOH1160 / AOH1996 | ||||||
Function / homology | ![]() positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis ...positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / replisome / response to L-glutamate / histone acetyltransferase binding / DNA polymerase processivity factor activity / G1/S-Specific Transcription / leading strand elongation / response to dexamethasone / replication fork processing / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / cyclin-dependent protein kinase holoenzyme complex / mismatch repair / translesion synthesis / response to cadmium ion / DNA polymerase binding / epithelial cell differentiation / positive regulation of DNA repair / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair, gap-filling / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / replication fork / positive regulation of DNA replication / male germ cell nucleus / liver regeneration / nuclear estrogen receptor binding / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / receptor tyrosine kinase binding / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / chromosome, telomeric region / damaged DNA binding / nuclear body / centrosome / chromatin binding / protein-containing complex binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jossart, J. / Perry, J.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Small molecule targeting of transcription-replication conflict for selective chemotherapy. Authors: Gu, L. / Li, M. / Li, C.M. / Haratipour, P. / Lingeman, R. / Jossart, J. / Gutova, M. / Flores, L. / Hyde, C. / Kenjic, N. / Li, H. / Chung, V. / Li, H. / Lomenick, B. / Von Hoff, D.D. / ...Authors: Gu, L. / Li, M. / Li, C.M. / Haratipour, P. / Lingeman, R. / Jossart, J. / Gutova, M. / Flores, L. / Hyde, C. / Kenjic, N. / Li, H. / Chung, V. / Li, H. / Lomenick, B. / Von Hoff, D.D. / Synold, T.W. / Aboody, K.S. / Liu, Y. / Horne, D. / Hickey, R.J. / Perry, J.J.P. / Malkas, L.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 199.3 KB | Display | ![]() |
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PDB format | ![]() | 159.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 36.2 KB | Display | |
Data in CIF | ![]() | 47.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gl9C ![]() 3vkxS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28795.752 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZQZ / #3: Chemical | ChemComp-CL / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.29 Å3/Da / Density % sol: 71.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M sodium cacodylate pH 6.5, 0.2 M sodium chloride, 2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.77→39.59 Å / Num. obs: 19342 / % possible obs: 99.6 % / Redundancy: 5.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.09 / Rrim(I) all: 0.221 / Χ2: 0.97 / Net I/σ(I): 6.9 / Num. measured all: 114061 |
Reflection shell | Resolution: 3.77→4.13 Å / % possible obs: 99.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.788 / Num. measured all: 27122 / Num. unique obs: 4598 / CC1/2: 0.774 / Rpim(I) all: 0.347 / Rrim(I) all: 0.862 / Χ2: 0.98 / Net I/σ(I) obs: 2.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VKX Resolution: 3.77→39.59 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.77→39.59 Å
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Refine LS restraints |
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LS refinement shell |
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