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Yorodumi- PDB-2avs: kinetics, stability, and structural changes in high resolution cr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2avs | ||||||
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Title | kinetics, stability, and structural changes in high resolution crystal structures of HIV-1 protease with drug resistant mutations L24I, I50V, and G73S | ||||||
Components | Pol polyprotein | ||||||
Keywords | HYDROLASE / DRUG RESISTANCE / HIV-1 PROTEASE / INDINAVIR / SUBSTRATE ANALOG / NON-ACTIVE SITE MUTANTS. | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / viral translational frameshifting / 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 | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Liu, F. / Boross, P.I. / Wang, Y.F. / Tozser, J. / Louis, J.M. / Harrison, R.W. / Weber, I.T. | ||||||
Citation | 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 | 2avs.cif.gz | 116.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2avs.ent.gz | 89.6 KB | Display | PDB format |
PDBx/mmJSON format | 2avs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2avs_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2avs_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2avs_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 2avs_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/2avs ftp://data.pdbj.org/pub/pdb/validation_reports/av/2avs | HTTPS FTP |
-Related structure data
Related structure data | 2avmC 2avoC 2avqC 2avvC 1dazS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10726.649 Da / Num. of mol.: 2 / Fragment: retropepsin Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH INDINAVIR / Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: GAG-POL / Production host: Escherichia coli (E. coli) / References: UniProt: P04587, HIV-1 retropepsin |
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-Non-polymers , 6 types, 327 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-DMS / | #5: Chemical | ChemComp-MK1 / | #6: Chemical | ChemComp-ACY / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.25 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: CITRATE/PHOSPHATE BUFFER, PH 5.8, SATURATED AMMONIUM SULPHATE, 30-35%, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 12, 2002 |
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: 1.1→50 Å / Num. all: 74154 / Num. obs: 72654 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 33.81 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 5.07 / % possible all: 85.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1DAZ Resolution: 1.1→10 Å / Num. parameters: 19103 / Num. restraintsaints: 24697 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 37 / Occupancy sum hydrogen: 1635 / Occupancy sum non hydrogen: 1825.7 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.14 Å |