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Yorodumi- PDB-3bvb: Cystal structure of HIV-1 Active Site Mutant D25N and inhibitor D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bvb | ||||||
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Title | Cystal structure of HIV-1 Active Site Mutant D25N and inhibitor Darunavir | ||||||
Components | Protease (Retropepsin) | ||||||
Keywords | HYDROLASE / DRUG RESISTANCE / HIV-1 / D25N / MUTANT / AIDS / Aspartyl protease / Capsid maturation / Core protein / DNA integration / DNA recombination / DNA-directed DNA polymerase / Endonuclease / Lipoprotein / Magnesium / Membrane / Metal-binding / Multifunctional enzyme / Myristate / Nuclease / Nucleotidyltransferase / Nucleus / Phosphoprotein / Protease / RNA-binding / RNA-directed DNA polymerase / Transferase / Viral nucleoprotein / Virion / Zinc-finger | ||||||
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 / SYNCHROTRON / AB INITIO / Resolution: 1.3 Å | ||||||
Authors | Liu, F. / Weber, I.T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Effect of the Active Site D25N Mutation on the Structure, Stability, and Ligand Binding of the Mature HIV-1 Protease. Authors: Sayer, J.M. / Liu, F. / Ishima, R. / Weber, I.T. / Louis, J.M. #1: Journal: J.Biol.Chem. / Year: 2003 Title: Solution structure of the mature HIV-1 protease monomer: insight into the tertiary fold and stability of a precursor. Authors: Ishima, R. / Torchia, D.A. / Lynch, S.M. / Gronenborn, A.M. / Louis, J.M. #2: Journal: J.Mol.Biol. / Year: 2005 Title: Kinetic, stability, and structural changes in high-resolution crystal structures of HIV-1 protease with drug-resistant mutations L24I, I50V, and G73S. Authors: Liu, F. / Boross, P.I. / Wang, Y.F. / Tozser, J. / Louis, J.M. / Harrison, R.W. / Weber, I.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bvb.cif.gz | 107.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bvb.ent.gz | 82.4 KB | Display | PDB format |
PDBx/mmJSON format | 3bvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/3bvb ftp://data.pdbj.org/pub/pdb/validation_reports/bv/3bvb | HTTPS FTP |
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-Related structure data
Related structure data | 3bvaC 1dazS C: citing same article (ref.) 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10739.691 Da / Num. of mol.: 2 / Mutation: Q7K,D25N, L33I, L63I, C67A, C97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03367, HIV-1 retropepsin |
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-Non-polymers , 5 types, 200 molecules
#2: Chemical | ChemComp-NA / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-017 / ( |
#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.15 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: SODIUM ACETATE BUFFER, 30% SODIUM CHLORIDE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 8, 2000 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. all: 51872 / Num. obs: 49278 / % possible obs: 89.8 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.2 / % possible all: 71.8 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: PDB entry 1DAZ Resolution: 1.3→10 Å / Num. parameters: 16939 / Num. restraintsaints: 21678 / Cross valid method: FREE R / σ(F): 0 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 22 / Occupancy sum hydrogen: 1635 / Occupancy sum non hydrogen: 1697.8 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→10 Å
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Refine LS restraints |
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