+Open data
-Basic information
Entry | Database: PDB / ID: 2zu4 | ||||||
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Title | Complex structure of SARS-CoV 3CL protease with TG-0204998 | ||||||
Components | 3C-like proteinase | ||||||
Keywords | hydrolase/hydrolase inhibitor / protease-inhibitor complex / Hydrolase / Protease / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information 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 / 5'-3' DNA helicase activity / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / methylation / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / 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 / virus-mediated perturbation of host defense response / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | SARS coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Hsu, M.F. / Lee, C.C. / Wang, A.H.-J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zu4.cif.gz | 79.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zu4.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zu4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/2zu4 ftp://data.pdbj.org/pub/pdb/validation_reports/zu/2zu4 | HTTPS FTP |
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-Related structure data
Related structure data | 2ztxC 2ztyC 2ztzC 2zu1C 2zu2C 2zu3C 2zu5C 1z1iS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33876.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS coronavirus / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) References: UniProt: P0C6U8, UniProt: P0C6X7*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Chemical | ChemComp-ZU3 / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | THE UNBOUND VERSION OF THE INHIBITOR HAS A DOUBLE BOND BETWEEN ATOMS C63 AND C82, WHICH OPENS UP ...THE UNBOUND VERSION OF THE INHIBITOR HAS A DOUBLE BOND BETWEEN ATOMS C63 AND C82, WHICH OPENS UP WHEN IT COVALENTLY |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 3~6% PEG 6000, 4~6% DMSO or MPD, 1mM DTT, 0.1M MES , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. all: 33640 / Num. obs: 31992 / % possible obs: 95.1 % / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.93→2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 4.78 / Num. unique all: 2841 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Z1I Resolution: 1.93→30 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 71.058 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 96.39 Å2 / Biso mean: 52.327 Å2 / Biso min: 25.67 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→30 Å
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Refine LS restraints |
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Xplor file |
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