+
Open data
-
Basic information
Entry | Database: PDB / ID: 2zu5 | ||||||
---|---|---|---|---|---|---|---|
Title | complex structure of SARS-CoV 3CL protease with TG-0205486 | ||||||
![]() | 3C-like proteinase | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / protease-inhibitor complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral transcription ...Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral transcription / viral genome replication / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / SARS-CoV-1 activates/modulates innate immune responses / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methylation / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hsu, M.F. / Lee, C.C. / Wang, A.H.-J. | ||||||
![]() | ![]() Title: Structural Basis of Inhibition Specificities of 3C and 3C-like Proteases by Zinc-coordinating and Peptidomimetic Compounds Authors: Lee, C.C. / Kuo, C.J. / Ko, T.P. / Hsu, M.F. / Tsui, Y.C. / Chang, S.C. / Yang, S. / Chen, S.J. / Chen, H.C. / Hsu, M.C. / Shih, S.R. / Liang, P.H. / Wang, A.H.-J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 86 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 62.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 800.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 807.7 KB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ztxC ![]() 2ztyC ![]() 2ztzC ![]() 2zu1C ![]() 2zu2C ![]() 2zu3C ![]() 2zu4C ![]() 1z1iS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 33876.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P0C6U8, UniProt: P0C6X7*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
---|---|
#2: Chemical | ChemComp-ZU5 / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | THE UNBOUND VERSION OF THE INHIBITOR HAS A DOUBLE BOND BETWEEN ATOMS C9 AND C11, WHICH OPENS UP ...THE UNBOUND VERSION OF THE INHIBITOR HAS A DOUBLE BOND BETWEEN ATOMS C9 AND C11, WHICH OPENS UP WHEN IT COVALENTLY |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.43 % |
---|---|
Crystal grow | Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 54044 / Num. obs: 51828 / % possible obs: 95.9 % / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 16.63 |
Reflection shell | Resolution: 1.65→1.77 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.13 / Num. unique all: 4986 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1Z1I Resolution: 1.65→26.25 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Bsol: 58.48 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 78.31 Å2 / Biso mean: 26.5 Å2 / Biso min: 11.67 Å2
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→26.25 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|