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- PDB-5eql: Isoform-specific inhibition of SUMO-dependent protein-protein int... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5eql | ||||||||||||
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Title | Isoform-specific inhibition of SUMO-dependent protein-protein interactions | ||||||||||||
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![]() | PROTEIN BINDING / Ubiquitin / Sumoylation | ||||||||||||
Function / homology | ![]() SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / protein sumoylation ...SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / SUMOylation of intracellular receptors / PML body / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Processing of DNA double-strand break ends / ubiquitin protein ligase binding / RNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||||||||
Biological species | synthetic construct (others)![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Hughes, D.J. / Tiede, C. / Hall, N. / Tang, A.A.S. / Trinh, C.H. / Zajac, K. / Mandal, U. / Howell, G. / Edwards, T.A. / McPherson, M.J. ...Hughes, D.J. / Tiede, C. / Hall, N. / Tang, A.A.S. / Trinh, C.H. / Zajac, K. / Mandal, U. / Howell, G. / Edwards, T.A. / McPherson, M.J. / Tomlinson, D.C. / Whitehouse, A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Generation of specific inhibitors of SUMO-1- and SUMO-2/3-mediated protein-protein interactions using Affimer (Adhiron) technology. Authors: Hughes, D.J. / Tiede, C. / Penswick, N. / Tang, A.A. / Trinh, C.H. / Mandal, U. / Zajac, K.Z. / Gaule, T. / Howell, G. / Edwards, T.A. / Duan, J. / Feyfant, E. / McPherson, M.J. / Tomlinson, ...Authors: Hughes, D.J. / Tiede, C. / Penswick, N. / Tang, A.A. / Trinh, C.H. / Mandal, U. / Zajac, K.Z. / Gaule, T. / Howell, G. / Edwards, T.A. / Duan, J. / Feyfant, E. / McPherson, M.J. / Tomlinson, D.C. / Whitehouse, A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.1 KB | Display | ![]() |
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PDB format | ![]() | 58.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5eljSC ![]() 5eluC ![]() 1wm3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13252.120 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Gene: PHYTOCYSTATIN / Plasmid: PET11 / Production host: ![]() ![]() |
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#2: Protein | Mass: 8965.129 Da / Num. of mol.: 1 / Fragment: UNP residues 14-89 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.13 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 0.1 M HEPES sodium salt pH 7.6, 22% w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2014 |
Radiation | Monochromator: SAGITALLY FOCUSED Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→64.32 Å / Num. obs: 6930 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.49→2.61 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 3.8 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1WM3 and 5ELJ Resolution: 2.49→64.32 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.926 / SU B: 23.882 / SU ML: 0.243 / Cross valid method: FREE R-VALUE / ESU R Free: 0.267 / 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: 67.427 Å2
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Refinement step | Cycle: 1 / Resolution: 2.49→64.32 Å
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Refine LS restraints |
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