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- PDB-5ezs: Venezuelan Equine Encephalitis Virus (VEEV) Nonstructural Protein... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ezs | ||||||
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Title | Venezuelan Equine Encephalitis Virus (VEEV) Nonstructural Protein 2 (nsP2) Cysteine Protease Inhibited by E64d | ||||||
![]() | Non-structural Protein 2 Cysteine Protease | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Papain-like Cysteine protease / Clan CN / E64d adduct / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() O-acetyl-ADP-ribose deacetylase activity / host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / poly(A) RNA polymerase activity / polynucleotide adenylyltransferase / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity ...O-acetyl-ADP-ribose deacetylase activity / host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / poly(A) RNA polymerase activity / polynucleotide adenylyltransferase / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / Transferases; Transferring one-carbon groups; Methyltransferases / host cell cytoplasmic vesicle membrane / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleoside-triphosphate phosphatase / methylation / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / GTP binding / host cell plasma membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Legler, P.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Kinetic, Mutational, and Structural Studies of the Venezuelan Equine Encephalitis Virus Nonstructural Protein 2 Cysteine Protease. Authors: Hu, X. / Compton, J.R. / Leary, D.H. / Olson, M.A. / Lee, M.S. / Cheung, J. / Ye, W. / Ferrer, M. / Southall, N. / Jadhav, A. / Morazzani, E.M. / Glass, P.J. / Marugan, J. / Legler, P.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.8 KB | Display | ![]() |
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PDB format | ![]() | 60.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 682.6 KB | Display | ![]() |
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Full document | ![]() | 683.7 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 22.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ezqC ![]() 2hwkS 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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Components
#1: Protein | Mass: 38341.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Trinidad donkey / Plasmid: pET32a / Production host: ![]() ![]() References: UniProt: P27282, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Chemical | ChemComp-E6D / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 43.87 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: JCSG+ Condition #8 (0.2 M Ammonium formate, 20% PEG 3350) |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Mar 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→60.89 Å / Num. obs: 18605 / % possible obs: 99.2 % / Redundancy: 7.3 % / Biso Wilson estimate: 16 Å2 / Rsym value: 0.0591 / Net I/σ(I): 14.16 |
Reflection shell | Resolution: 2.16→2.26 Å / Redundancy: 4.04 % / Rmerge(I) obs: 0.2655 / Mean I/σ(I) obs: 4.91 / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2HWK Resolution: 2.16→51.31 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.415 Å2
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Refinement step | Cycle: LAST / Resolution: 2.16→51.31 Å
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Refine LS restraints |
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