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Open data
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Basic information
Entry | Database: PDB / ID: 4pdw | ||||||
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Title | A benzonitrile analogue inhibits rhinovirus replication | ||||||
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![]() | VIRUS / benzonitrile inhibitor | ||||||
Function / homology | ![]() 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 ...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 / symbiont-mediated suppression of host gene expression / DNA replication / host cell cytoplasm / RNA helicase activity / 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 / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Querol-Audi, J. / Guerra, P. / Lacroix, C. / Roche, M. / Franco, D. / Froeyen, M. / Terme, T. / Vanelle, P. / Neyts, J. / Leyssen, P. / Verdaguer, N. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174.9 KB | Display | ![]() |
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PDB format | ![]() | 136.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 696.4 KB | Display | ![]() |
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Full document | ![]() | 710.1 KB | Display | |
Data in XML | ![]() | 31.7 KB | Display | |
Data in CIF | ![]() | 42.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hrvS 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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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) ![]() 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) ![]() 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) ![]() 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) ![]() |
-Non-polymers , 3 types, 74 molecules ![](data/chem/img/GOL.gif)
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#5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-2XK / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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