+Open data
-Basic information
Entry | Database: PDB / ID: 3s45 | ||||||
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Title | wild-type HIV-2 protease with antiviral drug amprenavir | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / AMPRENAVIR / HIV/AIDS / drug resistance / aspartic protease / molecular recognition / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Human immunodeficiency virus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Tie, Y.-F. / Wang, Y.-F. / Weber, I.T. | ||||||
Citation | Journal: Protein Sci. / Year: 2012 Title: Critical differences in HIV-1 and HIV-2 protease specificity for clinical inhibitors. Authors: Tie, Y. / Wang, Y.F. / Boross, P.I. / Chiu, T.Y. / Ghosh, A.K. / 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 | 3s45.cif.gz | 101.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s45.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 3s45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s45_validation.pdf.gz | 790.2 KB | Display | wwPDB validaton report |
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Full document | 3s45_full_validation.pdf.gz | 794.4 KB | Display | |
Data in XML | 3s45_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 3s45_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/3s45 ftp://data.pdbj.org/pub/pdb/validation_reports/s4/3s45 | HTTPS FTP |
-Related structure data
Related structure data | 3s43C 3s53C 3s54C 3s56C 3ebzS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10728.337 Da / Num. of mol.: 2 / Fragment: residues 514-612 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 2 / Strain: 11720 / Gene: pol / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9W9R3, HIV-2 retropepsin |
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-Non-polymers , 6 types, 121 molecules
#2: Chemical | ChemComp-NA / | ||||||||
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#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-IMD / #5: Chemical | ChemComp-ZN / #6: Chemical | ChemComp-478 / { | #7: 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: 2.15 Å3/Da / Density % sol: 42.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1.5 M NaCl, 0.6 M imidazole/0.12 M Zinc Acetate Buffer at pH 6.0. 30% glycerol as cryoprotector, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→50 Å / Num. all: 25917 / Num. obs: 25917 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.51→1.56 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1811 / % possible all: 63.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EBZ Resolution: 1.51→10 Å / Num. parameters: 15542 / Num. restraintsaints: 19854 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: conjugage gradient minimization
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Refine analyze | Num. disordered residues: 8 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1669.7 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→10 Å
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Refine LS restraints |
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