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Yorodumi- PDB-2avm: Kinetics, stability, and structural changes in high resolution cr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2avm | ||||||
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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 | HIV-1 protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HIV-1 PROTEASE / DRUG RESISTANCE / SUBSTRATE ANALOG / NON-ACTIVE SITE MUTANTS / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
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 / 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 | 2avm.cif.gz | 117.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2avm.ent.gz | 90.6 KB | Display | PDB format |
PDBx/mmJSON format | 2avm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/2avm ftp://data.pdbj.org/pub/pdb/validation_reports/av/2avm | HTTPS FTP |
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-Related structure data
Related structure data | 2avoC 2avqC 2avsC 2avvC 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 on special symmetry positions |
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-Components
#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 / Strain: Isolate BH5 / Gene: GAG-POL / Production host: Escherichia coli (E. coli) / References: UniProt: P04587, HIV-1 retropepsin #2: Chemical | #3: Chemical | ChemComp-2NC / | #4: Chemical | ChemComp-ACY / | #5: Water | ChemComp-HOH / | Sequence details | MUTATIONS Q7K, L33I, L63I, C67A, C95A, HAVE BEEN MADE TO STABILIZE THE PROTEASE FROM ...MUTATIONS Q7K, L33I, L63I, C67A, C95A, HAVE BEEN MADE TO STABILIZE THE PROTEASE FROM AUTOPROTEO | |
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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: 2.6 Å3/Da / Density % sol: 52.9 % |
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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, 5-10%,DMSO 13%, pH 5.80, 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: 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: 91188 / Num. obs: 90988 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 25.24 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 9.9 / % possible all: 84 |
-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: 19271 / Num. restraintsaints: 24738 / 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: 44 / Occupancy sum hydrogen: 1659 / Occupancy sum non hydrogen: 1837.76 | |||||||||||||||||||||||||||||||||
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 |