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Yorodumi- PDB-1heg: The crystal structures at 2.2 angstroms resolution of hydroxyethy... -
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-Basic information
Entry | Database: PDB / ID: 1heg | ||||||
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Title | The crystal structures at 2.2 angstroms resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations | ||||||
Components | HIV-1 PROTEASE | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / ACID PROTEINASE | ||||||
Function / homology | Function and homology information symbiont-mediated activation of host apoptosis / HIV-1 retropepsin / 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 ...symbiont-mediated activation of host apoptosis / HIV-1 retropepsin / 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 / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / viral translational frameshifting / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Murthy, K. / Winborne, E.L. / Minnich, M.D. / Culp, J.S. / Debouck, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1992 Title: The crystal structures at 2.2-A resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations. Authors: Murthy, K.H. / Winborne, E.L. / Minnich, M.D. / Culp, J.S. / Debouck, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1heg.cif.gz | 35.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1heg.ent.gz | 22.9 KB | Display | PDB format |
PDBx/mmJSON format | 1heg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1heg_validation.pdf.gz | 456.9 KB | Display | wwPDB validaton report |
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Full document | 1heg_full_validation.pdf.gz | 472.6 KB | Display | |
Data in XML | 1heg_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 1heg_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/1heg ftp://data.pdbj.org/pub/pdb/validation_reports/he/1heg | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUES PHE I 203, OHE I 203A, AND GLY I 204 REPRESENT PHE-PSI(CHOH-CH2)-GLY. THUS ATOMS C AND N OF PHE I 203 AND ATOM N OF GLY I 204 ARE NOT PRESENT AND ARE REPLACED BY THE ATOMS OF THE HET GROUP OHE. |
-Components
#1: Protein | Mass: 10786.663 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-PSI / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | THE SCISSILE BOND IN THE INHIBITOR PSI IS REPLACED BY A HYDROXYETHYLENE ISOSTERE (CHOH-CH2) THE ...THE SCISSILE BOND IN THE INHIBITOR PSI IS REPLACED BY A HYDROXYETH |
Sequence details | THIS VARIANT OF THE HIV 1 PROTEASE HAS ASN 36 AS CONFIRMED BY INSPECTION OF THE ELECTRON DENSITY. ...THIS VARIANT OF THE HIV 1 PROTEASE HAS ASN 36 AS CONFIRMED BY INSPECTION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.96 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 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 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.2→5 Å / σ(I): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.2→5 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.186 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |