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Yorodumi- PDB-5f6y: Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment... -
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-Basic information
Entry | Database: PDB / ID: 5f6y | ||||||
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Title | Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole) | ||||||
Components | SUMO-conjugating enzyme UBC9 | ||||||
Keywords | LIGASE/LIGASE inhibitor / Ubc9 / Fragment drug design / sumoylation / LIGASE-LIGASE inhibitor complex | ||||||
Function / homology | Function and homology information positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / SUMOylation of nuclear envelope proteins / transferase complex / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / mitotic nuclear membrane reassembly / Vitamin D (calciferol) metabolism ...positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / SUMOylation of nuclear envelope proteins / transferase complex / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / mitotic nuclear membrane reassembly / Vitamin D (calciferol) metabolism / synaptonemal complex / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / nuclear export / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / SUMOylation of chromatin organization proteins / SUMOylation of ubiquitinylation proteins / transcription factor binding / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA damage response and repair proteins / nuclear pore / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Meiotic synapsis / transcription coregulator binding / SUMOylation of transcription cofactors / SUMOylation of intracellular receptors / chromosome segregation / protein modification process / PKR-mediated signaling / PML body / Formation of Incision Complex in GG-NER / nuclear envelope / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / ubiquitin-dependent protein catabolic process / positive regulation of cell migration / cell division / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å | ||||||
Authors | Lountos, G.T. / Hewitt, W.M. / Zlotkowski, K. / Dahlhauser, S. / Saunders, L.B. / Needle, D. / Tropea, J.E. / Zhan, C. / Wei, G. / Ma, B. ...Lountos, G.T. / Hewitt, W.M. / Zlotkowski, K. / Dahlhauser, S. / Saunders, L.B. / Needle, D. / Tropea, J.E. / Zhan, C. / Wei, G. / Ma, B. / Nussinov, R. / Schneekloth, J.S.Jr. / Waugh, D.S. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2016 Title: Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9. Authors: Hewitt, W.M. / Lountos, G.T. / Zlotkowski, K. / Dahlhauser, S.D. / Saunders, L.B. / Needle, D. / Tropea, J.E. / Zhan, C. / Wei, G. / Ma, B. / Nussinov, R. / Waugh, D.S. / Schneekloth, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f6y.cif.gz | 90.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f6y.ent.gz | 67.8 KB | Display | PDB format |
PDBx/mmJSON format | 5f6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f6y_validation.pdf.gz | 439.9 KB | Display | wwPDB validaton report |
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Full document | 5f6y_full_validation.pdf.gz | 441.1 KB | Display | |
Data in XML | 5f6y_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 5f6y_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/5f6y ftp://data.pdbj.org/pub/pdb/validation_reports/f6/5f6y | HTTPS FTP |
-Related structure data
Related structure data | 5f6dC 5f6eC 5f6uC 5f6vC 5f6wC 5f6xC 1u9bS 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: 17725.375 Da / Num. of mol.: 1 / Mutation: K48A,K49A,E54A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2I, UBC9, UBCE9 / Plasmid: pDN2405 / Production host: Escherichia coli (E. coli) References: UniProt: P63279, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Chemical | ChemComp-5VM / |
#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: 2.71 Å3/Da / Density % sol: 54.68 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol 8000 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→50 Å / Num. obs: 65740 / % possible obs: 94.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 1.14→1.16 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3 / % possible all: 67.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U9B Resolution: 1.14→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.978 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.817 Å2
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Refinement step | Cycle: 1 / Resolution: 1.14→50 Å
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