+Open data
-Basic information
Entry | Database: PDB / ID: 4pdw | ||||||
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Title | A benzonitrile analogue inhibits rhinovirus replication | ||||||
Components |
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Keywords | VIRUS / benzonitrile inhibitor | ||||||
Function / homology | Function and homology information lysis of host organelle involved in viral entry into host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...lysis of host organelle involved in viral entry into host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / host cell cytoplasm / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Human rhinovirus 14 Rhinovirus B | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Querol-Audi, J. / Guerra, P. / Lacroix, C. / Roche, M. / Franco, D. / Froeyen, M. / Terme, T. / Vanelle, P. / Neyts, J. / Leyssen, P. / Verdaguer, N. | ||||||
Citation | Journal: J.Antimicrob.Chemother. / Year: 2014 Title: A novel benzonitrile analogue inhibits rhinovirus replication. Authors: Lacroix, C. / Querol-Audi, J. / Roche, M. / Franco, D. / Froeyen, M. / Guerra, P. / Terme, T. / Vanelle, P. / Verdaguer, N. / Neyts, J. / Leyssen, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pdw.cif.gz | 174.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pdw.ent.gz | 136.7 KB | Display | PDB format |
PDBx/mmJSON format | 4pdw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/4pdw ftp://data.pdbj.org/pub/pdb/validation_reports/pd/4pdw | HTTPS FTP |
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-Related structure data
Related structure data | 1hrvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 4 types, 4 molecules ABCD
#1: Protein | Mass: 32560.549 Da / Num. of mol.: 1 / Fragment: resdiues 568-856 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 References: UniProt: P03303, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
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#2: Protein | Mass: 28501.361 Da / Num. of mol.: 1 / Fragment: resdiues 70-331 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 References: UniProt: P03303, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
#3: Protein | Mass: 26236.754 Da / Num. of mol.: 1 / Fragment: resdiues 332-657 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 References: UniProt: P03303, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
#4: Protein | Mass: 7183.863 Da / Num. of mol.: 1 / Fragment: residue 2-69 / Source method: isolated from a natural source / Source: (natural) Rhinovirus B / References: UniProt: F5A5A0 |
-Non-polymers , 3 types, 74 molecules
#5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-2XK / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: PEG 8000, calcium chloride |
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-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 3→49.75 Å / Num. obs: 553702 / % possible obs: 99.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.203 / Rsym value: 0.233 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.3 / Num. unique all: 80647 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HRV Resolution: 3→49.75 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 3→49.75 Å
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