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- PDB-2gz7: Structure-Based Drug Design and Structural Biology Study of Novel... -
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Basic information
Entry | Database: PDB / ID: 2gz7 | ||||||
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Title | Structure-Based Drug Design and Structural Biology Study of Novel Nonpeptide Inhibitors of SARS-CoV Main Protease | ||||||
![]() | Replicase polyprotein 1ab | ||||||
![]() | HYDROLASE / SARS CoV main protease | ||||||
Function / homology | ![]() viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / endopeptidase complex / endoribonuclease complex ...viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / endopeptidase complex / endoribonuclease complex / : / mRNA capping enzyme complex / suppression by virus of host type I interferon production / positive stranded viral RNA replication / positive regulation of RNA biosynthetic process / protein K48-linked deubiquitination / : / : / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / protein K63-linked deubiquitination / 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 / RNA-templated transcription / SARS-CoV-1 modulates host translation machinery / viral transcription / protein autoprocessing / 7-methylguanosine mRNA capping / positive regulation of viral genome replication / DNA helicase activity / Transferases; Transferring one-carbon groups; Methyltransferases / helicase activity / protein processing / SARS-CoV-1 activates/modulates innate immune responses / double-stranded RNA binding / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / ISG15-specific peptidase activity / double membrane vesicle viral factory outer membrane / symbiont-mediated suppression of host gene expression / 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 / symbiont-mediated suppression of host toll-like receptor signaling pathway / 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 / 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 / host cell cytoplasm / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / membrane => GO:0016020 / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / protein dimerization activity / 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 | ![]() ![]() ![]() | ||||||
![]() | Lu, I.L. / Wu, S.Y. | ||||||
![]() | ![]() Title: Structure-Based Drug Design and Structural Biology Study of Novel Nonpeptide Inhibitors of Severe Acute Respiratory Syndrome Coronavirus Main Protease Authors: Lu, I.L. / Mahindroo, N. / Liang, P.H. / Peng, Y.H. / Kuo, C.J. / Tsai, K.C. / Hsieh, H.P. / Chao, Y.S. / Wu, S.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.1 KB | Display | ![]() |
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PDB format | ![]() | 58.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 943.5 KB | Display | ![]() |
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Full document | ![]() | 949.2 KB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2gz8C ![]() 2gz9C ![]() 1uk4S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33876.637 Da / Num. of mol.: 1 / Fragment: 3C-like proteinase Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P59641, UniProt: P0C6X7*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Chemical | ChemComp-D3F / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2mM DTT, 6% PEG 6000, 0.1M Mes, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.856→30 Å / Num. all: 35887 / Num. obs: 37781 / % possible obs: 98.263 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.856→1.904 Å / % possible all: 95.37 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UK4; chain_id A Resolution: 1.856→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.856→30 Å
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Refine LS restraints |
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