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Open data
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Basic information
Entry | Database: PDB / ID: 1y6l | ||||||
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Title | Human ubiquitin conjugating enzyme E2E2 | ||||||
![]() | Ubiquitin-conjugating enzyme E2E2 | ||||||
![]() | LIGASE / Structural Genomics Consortium / UBIQUITIN / UBIQUITIN-CONJUGATING ENZYME / SGC | ||||||
Function / homology | ![]() ISG15 transferase activity / ISG15-protein conjugation / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / positive regulation of G1/S transition of mitotic cell cycle / protein K48-linked ubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation ...ISG15 transferase activity / ISG15-protein conjugation / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / positive regulation of G1/S transition of mitotic cell cycle / protein K48-linked ubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / DNA damage response / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Walker, J.R. / Avvakumov, G.V. / Newman, E.M. / Mackenzie, F. / Kozieradzki, I. / Bochkarev, A. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen. Authors: Sheng, Y. / Hong, J.H. / Doherty, R. / Srikumar, T. / Shloush, J. / Avvakumov, G.V. / Walker, J.R. / Xue, S. / Neculai, D. / Wan, J.W. / Kim, S.K. / Arrowsmith, C.H. / Raught, B. / Dhe-Paganon, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.3 KB | Display | ![]() |
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PDB format | ![]() | 80.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.6 KB | Display | ![]() |
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Full document | ![]() | 450 KB | Display | |
Data in XML | ![]() | 22 KB | Display | |
Data in CIF | ![]() | 32.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yh2C ![]() 1yrvC ![]() 1zdnC ![]() 1zuoC ![]() 2a4dC ![]() 2a7lC ![]() 2awfC ![]() 2f4wC ![]() 2ob4C ![]() 2qgxC ![]() 2z5dC ![]() 3bzhC ![]() 3cegC ![]() 1qcqS 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The biological unit is expected to be a monomer. |
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Components
#1: Protein | Mass: 16613.947 Da / Num. of mol.: 3 / Fragment: Residues 55-201 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 46.95 % |
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Crystal grow | Temperature: 298 K / pH: 8.5 Details: 2M (NH4)2SO4, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 22, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→19.26 Å / Num. obs: 39009 / % possible obs: 90.5 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 23.28 |
Reflection shell | Resolution: 1.85→1.92 Å / % possible all: 91.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QCQ Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.315 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.154 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.993 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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