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Yorodumi- PDB-1hvk: INFLUENCE OF STEREOCHEMISTRY ON ACTIVITY AND BINDING MODES FOR C2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hvk | ||||||
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Title | INFLUENCE OF STEREOCHEMISTRY ON ACTIVITY AND BINDING MODES FOR C2 SYMMETRY-BASED DIOL INHIBITORS OF HIV-1 PROTEASE | ||||||
Components | HIV-1 PROTEASE | ||||||
Keywords | HYDROLASE(ACID PROTEASE) | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Bhat, T.N. / Hosur, M.V. / Baldwin, E.T. / Erickson, J.W. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 1994 Title: Influence of Stereochemistry on Activity and Binding Modes for C2 Symmetry-Based Diol Inhibitors of HIV-1 Protease Authors: Hosur, M.V. / Bhat, T.N. / Kempf, D. / Baldwin, E.T. / Liu, B. / Gulnik, S. / Wideburg, N.E. / Norbeck, D.W. / Appelt, K. / Erickson, J.W. #1: Journal: Annu.Rev.Biochem. / Year: 1993 Title: Structure-Based Inhibitors of HIV-1 Protease Authors: Wlodawer, A. / Erickson, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hvk.cif.gz | 58.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hvk.ent.gz | 43 KB | Display | PDB format |
PDBx/mmJSON format | 1hvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hvk_validation.pdf.gz | 446 KB | Display | wwPDB validaton report |
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Full document | 1hvk_full_validation.pdf.gz | 448 KB | Display | |
Data in XML | 1hvk_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 1hvk_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/1hvk ftp://data.pdbj.org/pub/pdb/validation_reports/hv/1hvk | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: THE INHIBITOR A79 800 IS MISSING 10 HYDROGEN ATOMS. |
-Components
#1: Protein | Mass: 10803.756 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03366 #2: Chemical | ChemComp-A79 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.6 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 4.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
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: 1.8 Å / Lowest resolution: 7 Å / Num. all: 85425 / Num. obs: 16239 / Rmerge(I) obs: 0.0836 |
-Processing
Software |
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Refinement | Resolution: 1.8→7 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 1.8→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.177 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.63 |