+
Open data
-
Basic information
Entry | Database: PDB / ID: 6cp0 | ||||||
---|---|---|---|---|---|---|---|
Title | SdcA in complex with the E2, UbcH5C | ||||||
![]() |
| ||||||
![]() | LIGASE / Complex / Bacterial E3 Ligase / E2 | ||||||
Function / homology | ![]() (E3-independent) E2 ubiquitin-conjugating enzyme / Signaling by BMP / protein K6-linked ubiquitination / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / negative regulation of BMP signaling pathway / protein autoubiquitination ...(E3-independent) E2 ubiquitin-conjugating enzyme / Signaling by BMP / protein K6-linked ubiquitination / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / negative regulation of BMP signaling pathway / protein autoubiquitination / protein K48-linked ubiquitination / ubiquitin ligase complex / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / protein modification process / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endosome membrane / protein ubiquitination / DNA repair / apoptotic process / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wasilko, D.J. / Huang, Q. / Mao, Y. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Insights into the ubiquitin transfer cascade catalyzed by theLegionellaeffector SidC. Authors: Wasilko, D.J. / Huang, Q. / Mao, Y. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 276.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 225.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 445.6 KB | Display | |
Data in XML | ![]() | 24.9 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6cp2C ![]() 4trgS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 62006.695 Da / Num. of mol.: 1 / Mutation: C45A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 16874.305 Da / Num. of mol.: 1 / Mutation: C85S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P61077, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.72 Å3/Da / Density % sol: 66.94 % / Description: Small, plate-like crystals |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5 M ammonium sulfate, 3% glycerol, 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 80 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6309 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 25193 / % possible obs: 96.4 % / Redundancy: 4 % / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.9→2.95 Å |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4TRG Resolution: 3.01→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.892 / SU B: 42.876 / SU ML: 0.347 / Cross valid method: THROUGHOUT / ESU R Free: 0.408 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 80.161 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.01→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|