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- PDB-2hwd: A COMPARISON OF THE ANTI-RHINOVIRAL DRUG BINDING POCKET IN HRV14 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2hwd | |||||||||
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Title | A COMPARISON OF THE ANTI-RHINOVIRAL DRUG BINDING POCKET IN HRV14 AND HRV1A | |||||||||
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![]() | VIRUS / RHINOVIRUS COAT PROTEIN / Icosahedral virus | |||||||||
Function / homology | ![]() 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 ...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 / symbiont-mediated suppression of host gene expression / DNA replication / 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 Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Kim, K.H. / Rossmann, M.G. | |||||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.5 KB | Display | ![]() |
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PDB format | ![]() | 114.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.3 KB | Display | ![]() |
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Full document | ![]() | 603.6 KB | Display | |
Data in XML | ![]() | 34.2 KB | Display | |
Data in CIF | ![]() | 47.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Atom site foot note | 1: LYS 1 98 - TRP 1 99 OMEGA = 216.48 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: PRO 1 150 - GLY 1 151 OMEGA = 251.74 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: CIS PROLINE - PRO 3 93 / 4: CIS PROLINE - PRO 3 235 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 32610.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 29114.764 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 26176.998 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Protein/peptide | Mass: 4583.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#5: Chemical | ChemComp-W91 / |
Nonpolymer details | WIN56291 IS 5-(3-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL) PHENOXY)PROPYL)-3-METHYL ISOXAZOLE. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, hanging dropDetails: referred to 'Arnold,E.', (1984) J. Mol. Biol., 177, 417-430 | ||||||||||||||||||||||||||||||||||||||||||||||||
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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: 3.8 Å / Num. obs: 50500 / Redundancy: 1.66 % / Rmerge(I) obs: 0.135 |
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Processing
Refinement | Highest resolution: 3.8 Å Details: THIS STRUCTURE OF HUMAN RHINOVIRUS 1A COMPLEXED WITH A DRUG HAS NOT BEEN REFINED. RESIDUES CLOSE TO THE DRUG HAVE BEEN MODELED DIFFERENTLY THAN IN THE NATIVE STRUCTURE DUE TO VARIOUS ...Details: THIS STRUCTURE OF HUMAN RHINOVIRUS 1A COMPLEXED WITH A DRUG HAS NOT BEEN REFINED. RESIDUES CLOSE TO THE DRUG HAVE BEEN MODELED DIFFERENTLY THAN IN THE NATIVE STRUCTURE DUE TO VARIOUS CONFORMATIONAL CHANGES THAT OCCURRED UPON THE DRUG ENTRY. OTHER RESIDUES HAVE BEEN LEFT AT THE SAME POSITION AS IN THE NATIVE STRUCTURE. | ||||||||||||
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Refinement step | Cycle: LAST / Highest resolution: 3.8 Å
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