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Yorodumi- PDB-2hwc: A COMPARISON OF THE ANTI-RHINOVIRAL DRUG BINDING POCKET IN HRV14 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hwc | |||||||||
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Title | A COMPARISON OF THE ANTI-RHINOVIRAL DRUG BINDING POCKET IN HRV14 AND HRV1A | |||||||||
Components |
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Keywords | VIRUS / RHINOVIRUS COAT PROTEIN / Icosahedral virus | |||||||||
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 / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / 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 Similarity search - Function | |||||||||
Biological species | Human rhinovirus 14 | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | |||||||||
Authors | Kim, K.H. / Rossmann, M.G. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1993 Title: A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A. Authors: Kim, K.H. / Willingmann, P. / Gong, Z.X. / Kremer, M.J. / Chapman, M.S. / Minor, I. / Oliveira, M.A. / Rossmann, M.G. / Andries, K. / Diana, G.D. / Dutko, F.J. / McKinlay, M.A. / Pevear, D.C. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Human Rhinovirus 14 Complexed with Antiviral Compound R 61837 Authors: Chapman, M.S. / Minor, I. / Rossmann, M.G. / Diana, G.D. / Andries, K. #2: Journal: J.Mol.Biol. / Year: 1989 Title: Crystal Structure of Human Rhinovirus Serotype 1A (Hrv1A) Authors: Kim, S. / Smith, T.J. / Chapman, M.S. / Rossmann, M.G. / Pevear, D.C. / Dutko, F.J. / Felock, P.J. / Diana, G.D. / Mckinlay, M.A. #3: Journal: Biochemistry / Year: 1988 Title: Structural Analysis of a Series of Antiviral Agents Complexed with Human Rhinovirus 14 Authors: Badger, J. / Minor, I. / Kremer, M.J. / Oliveira, M.A. / Smith, T.J. / Griffith, J.P. / Guerin, D.M.A. / Krishnaswamy, S. / Luo, M. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Dutko, F. ...Authors: Badger, J. / Minor, I. / Kremer, M.J. / Oliveira, M.A. / Smith, T.J. / Griffith, J.P. / Guerin, D.M.A. / Krishnaswamy, S. / Luo, M. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Dutko, F.J. / Fancher, M. / Rueckert, R.R. / Heinz, B.A. #4: Journal: Science / Year: 1986 Title: The Site of Attachment in Human Rhinovirus 14 for Antiviral Agents that Inhibit Uncoating Authors: Smith, T.J. / Kremer, M.J. / Luo, M. / Vriend, G. / Arnold, E. / Kamer, G. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Otto, M.J. #5: Journal: Nature / Year: 1985 Title: Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses Authors: Rossmann, M.G. / Arnold, E. / Erickson, J.W. / Frankenberger, E.A. / Griffith, J.P. / Hecht, H.-J. / Johnson, J.E. / Kamer, G. / Luo, M. / Mosser, A.G. / Rueckert, R.R. / Sherry, B. / Vriend, G. | |||||||||
History |
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Remark 700 | SHEET THERE IS A BIFURCATED SHEET IN EACH OF CHAINS *1*, *2*, AND *3*. TO REPRESENT THIS FEATURE, ...SHEET THERE IS A BIFURCATED SHEET IN EACH OF CHAINS *1*, *2*, AND *3*. TO REPRESENT THIS FEATURE, REDUNDANT SHEETS ARE DEFINED. THUS SHEETS B11 AND B12 DIFFER ONLY IN STRAND 4, SHEETS B12 AND B22 DIFFER ONLY IN STRAND 4, AND SHEETS B13 AND B23 DIFFER IN STRANDS 1 AND 4 (DOUBLY BIFURCATED). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hwc.cif.gz | 152.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hwc.ent.gz | 117.1 KB | Display | PDB format |
PDBx/mmJSON format | 2hwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/2hwc ftp://data.pdbj.org/pub/pdb/validation_reports/hw/2hwc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 2 83 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 32560.549 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P03303 |
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#2: Protein | Mass: 28487.334 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P03303 |
#3: Protein | Mass: 26236.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P03303 |
#4: Protein | Mass: 7183.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P03303 |
#5: Chemical | ChemComp-W54 / |
Nonpolymer details | WIN54954 IS 5-(5-(2,6-DICHLORO-4-(4,5-DIHYDRO-2- OXAZOLYL)PHENOXY)PENTYL)-3-METHYL ISOXAZOLE. |
Sequence details | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.9 Å / Num. obs: 352588 / Redundancy: 11.1 % / Rmerge(I) obs: 0.111 |
-Processing
Refinement | Highest resolution: 3 Å | ||||||||||||
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Refinement step | Cycle: LAST / Highest resolution: 3 Å
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