+Open data
-Basic information
Entry | Database: PDB / ID: 3dox | ||||||
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Title | X-ray structure of HIV-1 protease in situ product complex | ||||||
Components |
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Keywords | HYDROLASE / HIV-1 protease / transition state / reaction intermediate / catalysis / inhibitor / X-ray Crystallography / AIDS / Aspartyl protease / Capsid maturation / Capsid protein / Cytoplasm / DNA integration / DNA recombination / DNA-directed DNA polymerase / Endonuclease / Host-virus interaction / Lipoprotein / Magnesium / Metal-binding / Multifunctional enzyme / Myristate / Nuclease / Nucleotidyltransferase / Nucleus / Phosphoprotein / Protease / Ribosomal frameshifting / RNA-binding / RNA-directed DNA polymerase / Transferase / Viral nucleoprotein / Virion / Zinc / Zinc-finger | ||||||
Function / homology | Function and homology information integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase 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 / structural molecule activity / host cell plasma membrane / virion membrane / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Hosur, M.V. / Ferrer, J.-L. / Das, A. / Prashar, V. / Bihani, S. | ||||||
Citation | Journal: Proteins / Year: 2009 Title: X-ray structure of HIV-1 protease in situ product complex Authors: Bihani, S. / Das, A. / Prashar, V. / Ferrer, J.-L. / Hosur, M.V. #1: Journal: Proteins / Year: 2001 Title: 1.9 A x-ray study shows closed flap conformation in crystals of tethered HIV-1 PR Authors: Pillai, B. / Kannan, K.K. / Hosur, M.V. #2: Journal: Biochem.J. / Year: 2005 Title: Observation of a tetrahedral reaction intermediate in the HIV-1 protease-substrate complex Authors: Kumar, M. / Prashar, V. / Mahale, S. / Hosur, M.V. #3: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Rapid screening for HIV-1 protease inhibitor leads through X-ray diffraction Authors: Pillai, B. / Kannan, K.K. / Bhat, S.V. / Hosur, M.V. #4: Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Crystal structure of HIV-1 protease in situ product complex and observation of a low-barrier hydrogen bond between catalytic aspartates Authors: Das, A. / Prashar, V. / Mahale, S. / Serre, L. / Ferrer, J.-L. / Hosur, M.V. | ||||||
History |
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Remark 600 | Some waters and the short peptide partially occupy the electron density. In some unit cells the ...Some waters and the short peptide partially occupy the electron density. In some unit cells the water cluster is there while in others the ligand is present. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dox.cif.gz | 54.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dox.ent.gz | 42.1 KB | Display | PDB format |
PDBx/mmJSON format | 3dox.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/3dox ftp://data.pdbj.org/pub/pdb/validation_reports/do/3dox | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 21902.760 Da / Num. of mol.: 1 / Mutation: C95M, C1095A Source method: isolated from a genetically manipulated source Details: TETHERED DIMER LINKED BY GGSSG Source: (gene. exp.) Human immunodeficiency virus type 1 (isolate HXB2 group M subtype B) Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P04585, HIV-1 retropepsin |
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#2: Protein/peptide | Mass: 510.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. |
#3: Protein/peptide | Mass: 327.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. |
#4: Water | ChemComp-HOH / |
Sequence details | THIS CONSTRUCT INCLUDES A LINKER THAT CONSIST OF 996TH GLY, 997TH GLY, 998TH SER, 999TH SER AND 1000TH GLY. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.27 % |
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Crystal grow | Temperature: 300 K / pH: 6.2 Details: 1-5% saturated ammonium sulfate, pH 6.2, Soaking, temperature 300.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97644 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 6, 2006 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97644 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 12272 / Num. obs: 12068 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.03 |
-Processing
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Refinement | Resolution: 2→45.11 Å / Occupancy max: 1 / Occupancy min: 0
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Solvent computation | Bsol: 77.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.13 Å2
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Refinement step | Cycle: LAST / Resolution: 2→45.11 Å
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Refine LS restraints |
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Xplor file |
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