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Yorodumi- PDB-1aid: STRUCTURE OF A NON-PEPTIDE INHIBITOR COMPLEXED WITH HIV-1 PROTEAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1aid | ||||||
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Title | STRUCTURE OF A NON-PEPTIDE INHIBITOR COMPLEXED WITH HIV-1 PROTEASE: DEVELOPING A CYCLE OF STRUCTURE-BASED DRUG DESIGN | ||||||
Components | HUMAN IMMUNODEFICIENCY VIRUS PROTEASE | ||||||
Keywords | HYDROLASE / PROTEASE / HIV / NON-PEPTIDE INHIBITOR / DRUG DESIGN | ||||||
Function / homology | Function and homology information 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 ...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 / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / 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 / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Rutenber, E.E. / Fauman, E.B. / Keenan, R.J. / Stroud, R.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1993 Title: Structure of a non-peptide inhibitor complexed with HIV-1 protease. Developing a cycle of structure-based drug design. Authors: Rutenber, E. / Fauman, E.B. / Keenan, R.J. / Fong, S. / Furth, P.S. / Ortiz de Montellano, P.R. / Meng, E. / Kuntz, I.D. / DeCamp, D.L. / Salto, R. / Rosb, J.R. / 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 | 1aid.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aid.ent.gz | 38.7 KB | Display | PDB format |
PDBx/mmJSON format | 1aid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/1aid ftp://data.pdbj.org/pub/pdb/validation_reports/ai/1aid | HTTPS FTP |
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-Related structure data
Related structure data | 2aidC 3hvpS S: Starting model for refinement C: citing same article (ref.) |
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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: 10800.712 Da / Num. of mol.: 2 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-CL / | #3: Chemical | ChemComp-THK / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.97 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: May 1, 1992 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→100 Å / Num. obs: 9988 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 |
Reflection | *PLUS Lowest resolution: 9999 Å / Num. measured all: 29425 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3HVP Resolution: 2.2→7 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.2→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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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