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Yorodumi- PDB-5vj3: HIV Protease (PR) in open form with Mg2+ in active site and HIVE-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vj3 | ||||||
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Title | HIV Protease (PR) in open form with Mg2+ in active site and HIVE-9 in eye site | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE / protease / allostery / fragment binding / eye site | ||||||
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 / establishment of integrated proviral latency / viral penetration into host nucleus ...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 / establishment of integrated proviral latency / viral penetration into host nucleus / 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 / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Tiefenbrunn, T. / Stout, C.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: to be published Title: Fragment-based campaign for the identification of potential exosite binders of HIV-1 Protease Authors: Forli, S. / Tiefenbrunn, T. / Baksh, M.M. / Chang, M.W. / Perryman, A. / Garg, D. / Happer, M. / Lin, Y.-C. / Goodsell, D. / Angelina, E.L. / De Vera, I. / Kojetin, D. / Torbett, B.E. / ...Authors: Forli, S. / Tiefenbrunn, T. / Baksh, M.M. / Chang, M.W. / Perryman, A. / Garg, D. / Happer, M. / Lin, Y.-C. / Goodsell, D. / Angelina, E.L. / De Vera, I. / Kojetin, D. / Torbett, B.E. / Finn, M.G. / Elder, J. / Stout, C.D. / Olson, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vj3.cif.gz | 38 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vj3.ent.gz | 23.3 KB | Display | PDB format |
PDBx/mmJSON format | 5vj3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vj3_validation.pdf.gz | 669.3 KB | Display | wwPDB validaton report |
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Full document | 5vj3_full_validation.pdf.gz | 672.5 KB | Display | |
Data in XML | 5vj3_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 5vj3_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/5vj3 ftp://data.pdbj.org/pub/pdb/validation_reports/vj/5vj3 | HTTPS FTP |
-Related structure data
Related structure data | 5vckC 5veaC 5w5wC 2pc0S 5to9 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
#1: Protein | Mass: 10767.702 Da / Num. of mol.: 1 / Fragment: UNP residues 4-102 / Mutation: Q1007K, L1033I, L1063I, C1067A, C1095A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: R8 / Gene: pol / Plasmid: PET 21A+ / Production host: Escherichia coli (E. coli) / Strain (production host): Bl2(DE3) References: UniProt: Q8Q8V9, UniProt: P12497*PLUS, HIV-1 retropepsin |
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#2: Chemical | ChemComp-HV9 / |
#3: Chemical | ChemComp-MG / |
#4: 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: 2.86 Å3/Da / Density % sol: 57.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.5 M NaCl, 0.2M MgCl2, 10mM Tris HCl pH 7.0, 10% DMSO, sat. HIVE9 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.9794 A | |||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 15, 2014 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2→35.47 Å / Num. obs: 9052 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.031 / Rrim(I) all: 0.082 / Net I/σ(I): 13 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PC0 Resolution: 2→35.47 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.961 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.176 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.36 Å2 / Biso mean: 49.628 Å2 / Biso min: 28.38 Å2
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Refinement step | Cycle: final / Resolution: 2→35.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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