[English] 日本語
Yorodumi- PDB-2avo: Kinetics, stability, and structural changes in high resolution cr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2avo | ||||||
---|---|---|---|---|---|---|---|
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 / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / viral penetration into host nucleus / establishment of integrated proviral latency ...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 / viral penetration into host nucleus / establishment of integrated proviral latency / 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 / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane / identical protein binding 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2avo.cif.gz | 114 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2avo.ent.gz | 87.7 KB | Display | PDB format |
PDBx/mmJSON format | 2avo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2avo_validation.pdf.gz | 818.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2avo_full_validation.pdf.gz | 823.9 KB | Display | |
Data in XML | 2avo_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 2avo_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/2avo ftp://data.pdbj.org/pub/pdb/validation_reports/av/2avo | HTTPS FTP |
-Related structure data
Related structure data | 2avmC 2avqC 2avsC 2avvC 1dazS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10740.677 Da / Num. of mol.: 2 / Fragment: protease retropepsin 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: P04587, UniProt: Q7SSI0*PLUS, HIV-1 retropepsin |
---|
-Non-polymers , 6 types, 270 molecules
#2: Chemical | ChemComp-SO4 / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-DMS / | ||||
#4: Chemical | ChemComp-MK1 / | ||||
#5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.1 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: CITRATE/PHOSPHATE BUFFER, PH 5.2, SATURATED AMMONIUM SULPHATE, 25%, VAPOR DIFFUSION, HANGING DROP, pH 5.20, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97105 / Wavelength: 0.97105 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 5, 2003 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97105 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. all: 76386 / Num. obs: 75564 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 28.23 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 7.38 / % possible all: 90 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1DAZ Resolution: 1.1→10 Å / Num. parameters: 18734 / Num. restraintsaints: 24835 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 45 / Occupancy sum hydrogen: 1639.06 / Occupancy sum non hydrogen: 1778.47 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.1→1.14 Å |