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- PDB-1ajv: HIV-1 PROTEASE IN COMPLEX WITH THE CYCLIC SULFAMIDE INHIBITOR AHA006 -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ajv | ||||||
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Title | HIV-1 PROTEASE IN COMPLEX WITH THE CYCLIC SULFAMIDE INHIBITOR AHA006 | ||||||
![]() | HIV-1 PROTEASE | ||||||
![]() | ASPARTYL PROTEASE / PROTEASE / NON-PEPTIDE INHIBITOR / DRUG DESIGN / HIV-1 | ||||||
Function / homology | ![]() 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 ...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 / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Backbro, K. / Unge, T. | ||||||
![]() | ![]() Title: Unexpected binding mode of a cyclic sulfamide HIV-1 protease inhibitor. Authors: Backbro, K. / Lowgren, S. / Osterlund, K. / Atepo, J. / Unge, T. / Hulten, J. / Bonham, N.M. / Schaal, W. / Karlen, A. / Hallberg, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.4 KB | Display | ![]() |
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PDB format | ![]() | 37.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 788.2 KB | Display | ![]() |
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Full document | ![]() | 787.2 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 13.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ajxC ![]() 4phvS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10803.756 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NMB / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 54.03 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 5.5 Details: CRYSTALLIZATION WAS PERFORMED BY VAPOR DIFFUSION. PROTEASE (2 MG/ML) AND INHIBITOR (40 MM IN DMSO) WAS MIXED IN A RATIO OF 1:1 AND SUBJECTED TO COCRYSTALLIZATION. DROPS CONSISTING OF 5 ...Details: CRYSTALLIZATION WAS PERFORMED BY VAPOR DIFFUSION. PROTEASE (2 MG/ML) AND INHIBITOR (40 MM IN DMSO) WAS MIXED IN A RATIO OF 1:1 AND SUBJECTED TO COCRYSTALLIZATION. DROPS CONSISTING OF 5 MICROLITERS OF THE PROTEASE-INHIBITOR MIXTURE PLUS 5 MICROLITERS OF THE CRYSTALLIZATION BUFFER (50 MM MES PH 5.5, 0.4 M NACL AND 0.02% (W/V) NAN3) WERE EQUILIBRATED AGAINST THE SAME BUFFER AT 4 DEGREES C., vapor diffusion, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusionDetails: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 278 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 14846 / % possible obs: 91.7 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.041 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.088 / % possible all: 80 |
Reflection | *PLUS Num. measured all: 73708 |
Reflection shell | *PLUS % possible obs: 80 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4PHV Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.088 |