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Yorodumi- PDB-1hte: X-RAY CRYSTALLOGRAPHIC STUDIES OF A SERIES OF PENICILLIN-DERIVED ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hte | ||||||
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Title | X-RAY CRYSTALLOGRAPHIC STUDIES OF A SERIES OF PENICILLIN-DERIVED ASYMMETRIC INHIBITORS OF HIV-1 PROTEASE | ||||||
Components | (HIV-1 PROTEASE) x 2 | ||||||
Keywords | HYDROLASE(ACID PROTEINASE) | ||||||
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 / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / 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: 2.8 Å | ||||||
Authors | Jhoti, H. / Wonacott, A. / Murray-Rust, P. | ||||||
Citation | Journal: Biochemistry / Year: 1994 Title: X-ray crystallographic studies of a series of penicillin-derived asymmetric inhibitors of HIV-1 protease. Authors: Jhoti, H. / Singh, O.M. / Weir, M.P. / Cooke, R. / Murray-Rust, P. / Wonacott, A. #1: Journal: J.Med.Chem. / Year: 1993 Title: A Series of Penicillin-Derived C2-Symmetric Inhibitors of HIV-1 Proteinase: Structural and Modeling Studies Authors: Wonacott, A. / Cooke, R. / Hayes, F.R. / Hayes, M.M. / Jhoti, H. / Mcmeekin, P. / Mistry, A. / Murray-Rust, P. / Singh, O.M.P. / Weir, M.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hte.cif.gz | 54.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hte.ent.gz | 39.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hte.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hte_validation.pdf.gz | 475.5 KB | Display | wwPDB validaton report |
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Full document | 1hte_full_validation.pdf.gz | 489.6 KB | Display | |
Data in XML | 1hte_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 1hte_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/1hte ftp://data.pdbj.org/pub/pdb/validation_reports/ht/1hte | 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: THE CONFORMATIONS OF THE SIDE CHAINS FOR RESIDUES SER A 37, ARG A 41, LYS A 43, GLN A 61, ILE A 72, AND SER B 37 ARE UNCLEAR. |
-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: Protein/peptide | | Mass: 475.493 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-G23 / ( | #4: Water | ChemComp-HOH / | Nonpolymer details | GR123976 IS (2R,4S)-2-[(R)-BENZYLCARBAMOYL- PHENYLACETYLAMINO-METHYL]-5,5-DIMETHYL-THIAZOLIDINE-4- ...GR123976 IS (2R,4S)-2-[(R)-BENZYLCARB | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.97 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 5.4 / PH range high: 3.4 | ||||||||||||||||||||||||
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: 2.8 Å / Num. obs: 5932 / % possible obs: 97 % / Rmerge(I) obs: 0.112 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.8→10 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 5915 / Rfactor all: 0.161 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |