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Yorodumi- PDB-3aid: A NEW CLASS OF HIV-1 PROTEASE INHIBITOR: THE CRYSTALLOGRAPHIC STR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aid | ||||||
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Title | A NEW CLASS OF HIV-1 PROTEASE INHIBITOR: THE CRYSTALLOGRAPHIC STRUCTURE, INHIBITION AND CHEMICAL SYNTHESIS OF AN AMINIMIDE PEPTIDE ISOSTERE | ||||||
Components | HUMAN IMMUNODEFICIENCY VIRUS PROTEASE | ||||||
Keywords | ASPARTYL PROTEASE / PROTEASE / HIV / PEPTIDE ISOSTERE INHIBITOR / DRUG DESIGN | ||||||
Function / homology | Function and homology information RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Rutenber, E.E. / Stroud, R.M. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 1996 Title: A new class of HIV-1 protease inhibitor: the crystallographic structure, inhibition and chemical synthesis of an aminimide peptide isostere. Authors: Rutenber, E.E. / McPhee, F. / Kaplan, A.P. / Gallion, S.L. / Hogan Jr., J.C. / Craik, C.S. / Stroud, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aid.cif.gz | 58.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aid.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 3aid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/3aid ftp://data.pdbj.org/pub/pdb/validation_reports/ai/3aid | HTTPS FTP |
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-Related structure data
Related structure data | 3hvpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10801.763 Da / Num. of mol.: 2 / Mutation: Q7K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Variant: SF1 ISOLATE / Production host: Escherichia coli (E. coli) / References: UniProt: P03369, HIV-1 retropepsin #2: Chemical | ChemComp-ARQ / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.04 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.4 / Details: pH 5.4 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. obs: 14215 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.7 Å / % possible obs: 61.1 % / Redundancy: 1.3 % / Num. possible: 1005 / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 6.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3HVP Resolution: 2.5→7 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.5→7 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 2 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.7 Å / Num. reflection Rfree: 1283 / Total num. of bins used: 5 / Rfactor obs: 0.259 |