[English] 日本語
![](img/lk-miru.gif)
- PDB-4wmd: Crystal structure of catalytically inactive MERS-CoV 3CL protease... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4wmd | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of catalytically inactive MERS-CoV 3CL protease (C148A) in spacegroup C2221 | ||||||
![]() | ORF1a | ||||||
![]() | HYDROLASE / 3CL protease / MERS / coronavirus | ||||||
Function / homology | ![]() host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity ...host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / proteolysis / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lountos, G.T. / Needle, D. / Waugh, D.S. | ||||||
![]() | ![]() Title: Structures of the Middle East respiratory syndrome coronavirus 3C-like protease reveal insights into substrate specificity. Authors: Needle, D. / Lountos, G.T. / Waugh, D.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 188.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 150.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 484.4 KB | Display | |
Data in XML | ![]() | 36.1 KB | Display | |
Data in CIF | ![]() | 50.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wmeC ![]() 4wmfC ![]() 2ynaS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 33322.109 Da / Num. of mol.: 3 / Mutation: C148A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pDN2551 / Production host: ![]() ![]() |
---|
-Non-polymers , 5 types, 291 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Chemical | ChemComp-1PE / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.28 Å3/Da / Density % sol: 71.3 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20.3 mg/mL protein, well solution: 0.1M Tris-Bis Tris pH 8.5, 0.12M ethylene glycols, 30% (v/v) ethylene glycol-polyethylene glycol 8000, (Morpheus Screeen condition E10). PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→50 Å / Num. obs: 53763 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rsym value: 0.077 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 2.58→2.62 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 2 / % possible all: 99.7 |
-
Processing
Software | Name: PHENIX / Version: (phenix.refine: dev_1448) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: pdb entry 2YNA chain A Resolution: 2.585→46.162 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 39.84 / Phase error: 23.01 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.585→46.162 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|