+Open data
-Basic information
Entry | Database: PDB / ID: 9f9m | ||||||
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Title | Crystal structure of MUS81-EME1 bound by compound 21. | ||||||
Components |
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Keywords | HYDROLASE / Endonuclease / fragment / drug discovery | ||||||
Function / homology | Function and homology information 3'-flap endonuclease activity / response to intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / osteoblast proliferation / Holliday junction resolvase complex / endodeoxyribonuclease complex / crossover junction DNA endonuclease activity / resolution of meiotic recombination intermediates / double-strand break repair via break-induced replication / DNA catabolic process ...3'-flap endonuclease activity / response to intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / osteoblast proliferation / Holliday junction resolvase complex / endodeoxyribonuclease complex / crossover junction DNA endonuclease activity / resolution of meiotic recombination intermediates / double-strand break repair via break-induced replication / DNA catabolic process / mitotic intra-S DNA damage checkpoint signaling / Resolution of D-loop Structures through Holliday Junction Intermediates / replication fork processing / nuclear replication fork / heterochromatin / replication fork / Fanconi Anemia Pathway / double-strand break repair / endonuclease activity / DNA repair / nucleolus / DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.469 Å | ||||||
Authors | Collie, G.W. | ||||||
Funding support | 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2024 Title: Fragment-Based Discovery of Novel MUS81 Inhibitors Authors: Collie, G.W. / Borjesson, U. / Chen, Y. / Dong, Z. / Di Fruscia, P. / Gohlke, A. / Hoyle, A. / Hunt, T.A. / Jesani, M.H. / Luo, H. / Luptak, J. / Milbradt, A.G. / Narasimhan, P. / Packer, M. ...Authors: Collie, G.W. / Borjesson, U. / Chen, Y. / Dong, Z. / Di Fruscia, P. / Gohlke, A. / Hoyle, A. / Hunt, T.A. / Jesani, M.H. / Luo, H. / Luptak, J. / Milbradt, A.G. / Narasimhan, P. / Packer, M. / Patel, S. / Qiao, J. / Storer, R.I. / Stubbs, C.J. / Tart, J. / Truman, C. / Wang, A.T. / Wheeler, M.G. / Winter-Holt, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9f9m.cif.gz | 146.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9f9m.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9f9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9f9m_validation.pdf.gz | 1015.1 KB | Display | wwPDB validaton report |
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Full document | 9f9m_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 9f9m_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 9f9m_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/9f9m ftp://data.pdbj.org/pub/pdb/validation_reports/f9/9f9m | HTTPS FTP |
-Related structure data
Related structure data | 9f98C 9f99C 9f9aC 9f9kC 9f9lC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34159.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MUS81 / Production host: Escherichia coli (E. coli) References: UniProt: Q96NY9, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters #2: Protein | Mass: 36144.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EME1, MMS4 / Production host: Escherichia coli (E. coli) References: UniProt: Q96AY2, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters #3: Chemical | ChemComp-MG / #4: Chemical | Mass: 315.324 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H17N3O4 / Feature type: SUBJECT OF INVESTIGATION Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15 % PEG10K, pH 6.5 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.47→50.23 Å / Num. obs: 34161 / % possible obs: 100 % / Redundancy: 3.4 % / CC1/2: 0.988 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.47→2.53 Å / Num. unique obs: 2525 / CC1/2: 0.751 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.469→50.23 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.908 / SU R Cruickshank DPI: 0.442 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.411 / SU Rfree Blow DPI: 0.293 / SU Rfree Cruickshank DPI: 0.305
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Displacement parameters | Biso mean: 75.63 Å2
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Refine analyze | Luzzati coordinate error obs: 0.56 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.469→50.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.47→2.49 Å
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