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- PDB-2aoj: Crystal structure analysis of HIV-1 protease with a substrate ana... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2aoj | ||||||
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Title | Crystal structure analysis of HIV-1 protease with a substrate analog P6-PR | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / HIV-1 PROTEASE / MUTANT / DIMER / SUBSTRATE ANALOG / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Tie, Y. / Boross, P.I. / Wang, Y.F. / Gaddis, L. / Liu, F. / Chen, X. / Tozser, J. / Harrison, R.W. / Weber, I.T. | ||||||
![]() | ![]() Title: Molecular basis for substrate recognition and drug resistance from 1.1 to 1.6 angstroms resolution crystal structures of HIV-1 protease mutants with substrate analogs. Authors: Tie, Y. / Boross, P.I. / Wang, Y.F. / Gaddis, L. / Liu, F. / Chen, X. / Tozser, J. / Harrison, R.W. / Weber, I.T. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.7 KB | Display | ![]() |
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PDB format | ![]() | 87.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 484.4 KB | Display | ![]() |
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Full document | ![]() | 493.9 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 19.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2aocC ![]() 2aodC ![]() 2aoeC ![]() 2aofC ![]() 2aogC ![]() 2aohC ![]() 2aoiC ![]() 1dazS C: citing same article ( S: Starting model for refinement |
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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
-Protein / Protein/peptide , 2 types, 3 molecules ABC
#1: Protein | Mass: 10740.677 Da / Num. of mol.: 2 / Fragment: HIV-1 PROTEASE (RETROPEPSIN) / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Strain: BH5 Isolate / Gene: POL / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Protein/peptide | | Mass: 1162.360 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: THIS SEQUENCE WAS CHEMICALLY SYNTHESIZED AND IS ANALOGOUS TO THE P6-PR PROCESSING SITE IN HIV-1. |
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-Non-polymers , 4 types, 162 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-ACY / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.46 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5 Details: AMMONIUM SULFATE 27%, DMSO 7%,SODIUM ACETATE BUFFER, pH 5.0, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99997 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 32284 / % possible obs: 99.1 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 4.3 / % possible all: 93.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 1DAZ Resolution: 1.6→10 Å / Num. parameters: 18116 / Num. restraintsaints: 24218 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 45 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1738.2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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