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- PDB-6kl6: Crystal structure of MERS-CoV N-NTD complexed with 5-Benzyloxygramine -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kl6 | ||||||
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Title | Crystal structure of MERS-CoV N-NTD complexed with 5-Benzyloxygramine | ||||||
![]() | Nucleoprotein | ||||||
![]() | VIRAL PROTEIN / Middle East respiratory syndrome coronavirus / nucleocapsid protein / N-terminal domain / 5-BENZYLOXYGRAMINE | ||||||
Function / homology | ![]() viral RNA genome packaging / negative regulation of interferon-beta production / viral capsid / host cell / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / ribonucleoprotein complex / RNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hou, M.H. / Lin, S.M. / Wang, Y.S. / Hsu, J.N. | ||||||
![]() | ![]() Title: Structure-Based Stabilization of Non-native Protein-Protein Interactions of Coronavirus Nucleocapsid Proteins in Antiviral Drug Design. Authors: Lin, S.M. / Lin, S.C. / Hsu, J.N. / Chang, C.K. / Chien, C.M. / Wang, Y.S. / Wu, H.Y. / Jeng, U.S. / Kehn-Hall, K. / Hou, M.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.7 KB | Display | ![]() |
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PDB format | ![]() | 80.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 785 KB | Display | ![]() |
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Full document | ![]() | 799 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kl2C ![]() 6kl5C ![]() 4j3kS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15855.566 Da / Num. of mol.: 4 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #2: Chemical | ChemComp-DJU / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 5 mg/mL protein, 25 mM Tris-HCl, pH 7.5, 75 mM NaCl, 70 mM MES, pH5.5, 37.5 M (NH4)2SO4, 14.5 % PEG 3350, 1 mM NaBr, 1 mM 5-Benzyloxygramine |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 14, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.76→30 Å / Num. obs: 17388 / % possible obs: 99.5 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.031 / Rrim(I) all: 0.079 / Χ2: 0.939 / Net I/σ(I): 11.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4J3K Resolution: 2.77→29.394 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 25.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.2 Å2 / Biso mean: 35.3863 Å2 / Biso min: 9.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.77→29.394 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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