+Open data
-Basic information
Entry | Database: PDB / ID: 3pwr | ||||||
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Title | HIV-1 Protease Mutant L76V complexed with Saquinavir | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HIV-1 / protease / mutation L76V / saquinavir / HYDROLASE / 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: 1.45 Å | ||||||
Authors | Zhang, Y. / Weber, I.T. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: The L76V Drug Resistance Mutation Decreases the Dimer Stability and Rate of Autoprocessing of HIV-1 Protease by Reducing Internal Hydrophobic Contacts. Authors: Louis, J.M. / Zhang, Y. / Sayer, J.M. / Wang, Y.F. / 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 | 3pwr.cif.gz | 107 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pwr.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 3pwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/3pwr ftp://data.pdbj.org/pub/pdb/validation_reports/pw/3pwr | HTTPS FTP |
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-Related structure data
Related structure data | 3pwmC 2nmyS 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
#1: Protein | Mass: 10726.650 Da / Num. of mol.: 2 / Fragment: residues 501-599 / Mutation: Q7K, L33I, L63I, C67A, L76V, C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03367, HIV-1 retropepsin #2: Chemical | ChemComp-ROC / ( | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-GOL / #5: 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: 2.73 Å3/Da / Density % sol: 54.98 % |
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Crystal grow | Temperature: 298 K / pH: 7 Details: CRYSTAL WAS GROWN BY THE HANGING-DROP VAPOR-DIFFUSION METHOD AT ROOM TEMPERATURE, FROM A 7 MG/ML PROTEIN SOLUTION AT PH 7.0 WITH 1.3 M NACL, 0.1 M TRIS-HCL, 3% DMSO. THE INHIBITOR WAS MIXED ...Details: CRYSTAL WAS GROWN BY THE HANGING-DROP VAPOR-DIFFUSION METHOD AT ROOM TEMPERATURE, FROM A 7 MG/ML PROTEIN SOLUTION AT PH 7.0 WITH 1.3 M NACL, 0.1 M TRIS-HCL, 3% DMSO. THE INHIBITOR WAS MIXED WITH PROTEASE IN A RATIO 5:1, VAPOR DIFFUSION HANGING DROP, TEMPERATURE 298K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 9, 2008 |
Radiation | Monochromator: SI220CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 38308 / % possible obs: 90.1 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 27.3 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.2 / % possible all: 56.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NMY Resolution: 1.45→10 Å / Num. parameters: 17050 / Num. restraintsaints: 10395 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT
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Refine analyze | Num. disordered residues: 12 / Occupancy sum hydrogen: 1648 / Occupancy sum non hydrogen: 1732.74 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→10 Å
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Refine LS restraints |
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