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Open data
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Basic information
Entry | Database: PDB / ID: 2yna | ||||||
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Title | Crystal structure of the main protease of coronavirus HKU4 | ||||||
![]() | 3C-LIKE PROTEINASE | ||||||
![]() | HYDROLASE / SARS | ||||||
Function / homology | ![]() host cell membrane / viral genome replication / methyltransferase activity / SARS coronavirus main proteinase / 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 ...host cell membrane / viral genome replication / methyltransferase activity / SARS coronavirus main proteinase / 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 / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease 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 / 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 | ![]() ![]() ![]() | ||||||
![]() | Ma, Q. / Xiao, Y. / Hilgenfeld, R. | ||||||
![]() | ![]() Title: Inhibitor for the Main Protease of Coronavirus Hku4 Authors: Ma, Q. / Xiao, Y. / Hilgenfeld, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 259.3 KB | Display | ![]() |
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PDB format | ![]() | 208.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.9 KB | Display | ![]() |
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Full document | ![]() | 452.1 KB | Display | |
Data in XML | ![]() | 31.3 KB | Display | |
Data in CIF | ![]() | 49.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ynbC ![]() 3tntS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.974, 0.1479, -0.1715), Vector: |
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Components
#1: Protein | Mass: 33220.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P0C6T4, SARS coronavirus main proteinase, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Chemical | #3: Chemical | ChemComp-IMD / | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Sequence details | 5XHIS TAG AT THE C-TERMINUS WAS DESIGNED, BUT IT SEEMS TO BE AUTO-CLEAVED BY THE PROTEASE IN THE ...5XHIS TAG AT THE C-TERMINUS WAS DESIGNED, BUT IT SEEMS TO BE AUTO-CLEAVED BY THE PROTEASE IN THE CRYSTAL, JUDGED BY THE ELECTRON DENSITY AT 1.5 A RESOLUTION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: SITTING-DROP VAPOR DIFFUSION AT 20C, 6% W/V POLYETHYLENE GLYCOL 3350, 2% V/V TACSIMATE, 5% V/V 2-PROPANOL, 0.1 M IMIDAZOLE PH 6.9. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 10, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→178.37 Å / Num. obs: 105128 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 17.75 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 32.4 |
Reflection shell | Resolution: 1.5→1.52 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4.3 / % possible all: 95.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3TNT Resolution: 1.5→68.96 Å / Cor.coef. Fo:Fc: 0.9636 / Cor.coef. Fo:Fc free: 0.9596 / SU R Cruickshank DPI: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.063 / SU Rfree Blow DPI: 0.062 / SU Rfree Cruickshank DPI: 0.06 Details: HYDROGEN ATOMS AT THEORETICAL THE REFINEMENT BUT REMOVED IN THIS DEPOSITED PDB. GERNERALLY MAIN CHAIN ATOMS ARE MODELED BASED ON CLEAR ELECTRON DENSITY.HOWEVER, SOME RESIDUES IN THE LOOP ...Details: HYDROGEN ATOMS AT THEORETICAL THE REFINEMENT BUT REMOVED IN THIS DEPOSITED PDB. GERNERALLY MAIN CHAIN ATOMS ARE MODELED BASED ON CLEAR ELECTRON DENSITY.HOWEVER, SOME RESIDUES IN THE LOOP REGION, WHICH SHOW SMALL GAP IN ELECTRON DENSITY, ARE MODELED STEREOCHEMICALLY. SIDE CHAIN ATOMS ARE MODELED BASED ON EITHER CLEAR ELECTRON DENSITY, OR STEREOCHEMICALLY WHEN THE ELECTRON DENSITY IS NOT DEFINED BUT THE MAIN CHAIN ATOMS OF THAT RESIDUE ARE MODELED.
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Displacement parameters | Biso mean: 22.68 Å2
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Refine analyze | Luzzati coordinate error obs: 0.157 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→68.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.54 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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