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Yorodumi- PDB-4ijh: Fragment-based Discovery of Protein-Protein Interaction Inhibitor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ijh | ||||||
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Title | Fragment-based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A | ||||||
Components | Replication protein A 70 kDa DNA-binding subunitDNA replication | ||||||
Keywords | DNA BINDING PROTEIN/INHIBITOR / OB-Fold / Protein-Protein Interaction / DNA BINDING PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / protein localization to site of double-strand break / Removal of the Flap Intermediate / single-stranded telomeric DNA binding / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding ...protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / protein localization to site of double-strand break / Removal of the Flap Intermediate / single-stranded telomeric DNA binding / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / telomere maintenance via telomerase / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / HSF1 activation / Regulation of HSF1-mediated heat shock response / mismatch repair / Activation of ATR in response to replication stress / SUMOylation of DNA damage response and repair proteins / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Gap-filling DNA repair synthesis and ligation in GG-NER / Translesion synthesis by POLI / meiotic cell cycle / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / double-strand break repair via homologous recombination / Translesion Synthesis by POLH / base-excision repair / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / Dual Incision in GG-NER / PML body / DNA-templated DNA replication / Meiotic recombination / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / single-stranded DNA binding / site of double-strand break / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / DNA replication / chromosome, telomeric region / damaged DNA binding / DNA repair / DNA damage response / nucleoplasm / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.498 Å | ||||||
Authors | Feldkamp, M.D. / Patrone, J.D. / Kennedy, J.P. / Frank, A.O. / Vangamudi, B. / Pelz, N.F. / Rossanese, O.W. / Waterson, A.G. / Fesik, S.W. / Chazin, W.J. | ||||||
Citation | Journal: ACS MED.CHEM.LETT. / Year: 2013 Title: Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A. Authors: Patrone, J.D. / Kennedy, J.P. / Frank, A.O. / Feldkamp, M.D. / Vangamudi, B. / Pelz, N.F. / Rossanese, O.W. / Waterson, A.G. / Chazin, W.J. / Fesik, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ijh.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ijh.ent.gz | 77.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ijh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/4ijh ftp://data.pdbj.org/pub/pdb/validation_reports/ij/4ijh | HTTPS FTP |
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-Related structure data
Related structure data | 4ijlC 2b29S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13497.728 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-120) / Mutation: E7R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: REPA1, RPA1, RPA70 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27694 | ||
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#2: Chemical | ChemComp-1EJ / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.88 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES, 200 mM calcium acetate, 15% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 7, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.498→50 Å / Num. obs: 18060 / % possible obs: 99.68 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 5.9 % / Biso Wilson estimate: 8.73 Å2 / Rsym value: 0.046 / Net I/σ(I): 16.65 |
Reflection shell | Resolution: 1.498→1.58 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 4.83 / Rsym value: 0.58 / % possible all: 96.99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2B29 Resolution: 1.498→37.865 Å / SU ML: 0.13 / σ(F): 1.35 / Phase error: 17.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.498→37.865 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: 12.476 Å / Origin y: -8.4692 Å / Origin z: 12.6363 Å
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Refinement TLS group | Selection details: all |