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Yorodumi- PDB-3s43: HIV-1 protease triple mutants V32I, I47V, V82I with antiviral dru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s43 | ||||||
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Title | HIV-1 protease triple mutants V32I, I47V, V82I with antiviral drug amprenavir | ||||||
Components | (Protease) x 2 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / AMPRENAVIR / HIV/AIDS / drug resistance / aspartic protease / molecular recognition / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information RNA-directed DNA polymerase activity / aspartic-type endopeptidase activity / proteolysis / identical protein binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å | ||||||
Authors | Wang, Y.-F. / Tie, 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 | 3s43.cif.gz | 104.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s43.ent.gz | 79.3 KB | Display | PDB format |
PDBx/mmJSON format | 3s43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/3s43 ftp://data.pdbj.org/pub/pdb/validation_reports/s4/3s43 | HTTPS FTP |
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-Related structure data
Related structure data | 3s45C 3s53C 3s54C 3s56C 3djkS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 10755.688 Da / Num. of mol.: 1 / Mutation: Q7K, V32I, L33I, I47V, L63I, C67A, V82I, 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: Q7SSE3, HIV-1 retropepsin |
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#2: Protein | Mass: 10754.703 Da / Num. of mol.: 1 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: Q7SSE3, UniProt: Q7SSI0*PLUS |
-Non-polymers , 4 types, 146 molecules
#3: Chemical | ChemComp-478 / { | ||||
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#4: Chemical | ChemComp-IOD / #5: Chemical | #6: 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: 2.72 Å3/Da / Density % sol: 54.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: FROM A 3.5MG/ML PROTEIN SOLUTION AT PH 5.4 WITH 0.175M KI, 0.1M CITRATE PHOSPHATE, 4% DMSO. 1.0ul WELL SOLUTION WITH 1.5ul PROTEIN SOLUTION. THE INHIBITOR WAS MIXED WITH PROTEASE IN A RATIO ...Details: FROM A 3.5MG/ML PROTEIN SOLUTION AT PH 5.4 WITH 0.175M KI, 0.1M CITRATE PHOSPHATE, 4% DMSO. 1.0ul WELL SOLUTION WITH 1.5ul PROTEIN SOLUTION. THE INHIBITOR WAS MIXED WITH PROTEASE IN A RATIO 5:1, EVAPORATION, 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 / Wavelength: 0.8 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 18, 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: 1.26→50 Å / Num. all: 58771 / Num. obs: 58771 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.26→1.31 Å / Redundancy: 2 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3786 / % possible all: 59.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DJK Resolution: 1.26→10 Å / Num. parameters: 16418 / Num. restraintsaints: 21829 / 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: 21 / Occupancy sum hydrogen: 1635 / Occupancy sum non hydrogen: 1662.6 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.26→10 Å
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Refine LS restraints |
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