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Yorodumi- PDB-3djk: Wild Type HIV-1 Protease with potent Antiviral inhibitor GRL-0255A -
+Open data
-Basic information
Entry | Database: PDB / ID: 3djk | ||||||
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Title | Wild Type HIV-1 Protease with potent Antiviral inhibitor GRL-0255A | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE / HIV-1 / wild type protease / protease inhibitor / AIDS / Aspartyl protease / Capsid maturation / Capsid protein / Cytoplasm / DNA integration / DNA recombination / DNA-directed DNA polymerase / Endonuclease / Lipoprotein / Magnesium / Metal-binding / Multifunctional enzyme / Myristate / Nuclease / Nucleotidyltransferase / Nucleus / Phosphoprotein / Protease / Ribosomal frameshifting / RNA-binding / RNA-directed DNA polymerase / Transferase / Viral nucleoprotein / Virion / Zinc / Zinc-finger | ||||||
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 type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||
Authors | Wang, Y.F. / Weber, I.T. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Flexible cyclic ethers/polyethers as novel P2-ligands for HIV-1 protease inhibitors: design, synthesis, biological evaluation, and protein-ligand X-ray studies Authors: Ghosh, A.K. / Gemma, S. / Baldridge, A. / Wang, Y.F. / Kovalevsky, A.Y. / Koh, Y. / Weber, I.T. / Mitsuya, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3djk.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3djk.ent.gz | 84.5 KB | Display | PDB format |
PDBx/mmJSON format | 3djk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3djk_validation.pdf.gz | 737 KB | Display | wwPDB validaton report |
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Full document | 3djk_full_validation.pdf.gz | 740.5 KB | Display | |
Data in XML | 3djk_validation.xml.gz | 13 KB | Display | |
Data in CIF | 3djk_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/3djk ftp://data.pdbj.org/pub/pdb/validation_reports/dj/3djk | HTTPS FTP |
-Related structure data
Related structure data | 2qciS 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
#1: Protein | Mass: 10740.677 Da / Num. of mol.: 2 / Fragment: UNP residues 501-599 Mutation: Q7K, L33I, L63I, C67A, C95A, Q107K, L133I, L163I, C167A, C195A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Gene: gag-pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) / References: UniProt: P03367, HIV-1 retropepsin #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-G55 / ( | #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: 2.68 Å3/Da / Density % sol: 54.15 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 4.2 Details: Crystal was grown by the hanging-drop vapor-diffusion method at r temperature, from a 2.0mg/ml protein solution at pH4.2 with 0.1M sodium acetate, 1.2M sodium chloride, 10% DMSO. The ...Details: Crystal was grown by the hanging-drop vapor-diffusion method at r temperature, from a 2.0mg/ml protein solution at pH4.2 with 0.1M sodium acetate, 1.2M sodium chloride, 10% DMSO. The inhibitor was mixed with protease in a ratio 15:1, EVAPORATION, 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 / Wavelength: 0.8 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 20, 2005 |
Radiation | Monochromator: SI 220 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1→50 Å / Num. all: 110362 / Num. obs: 110362 / % possible obs: 88.4 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1→1.04 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2.6 / % possible all: 52.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QCI Resolution: 1→10 Å / Num. parameters: 17846 / Num. restraintsaints: 24728 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT, THE CLOSE CONTACTS ARE DUE TO ALTERNATIVES
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 45 / Occupancy sum hydrogen: 1631 / Occupancy sum non hydrogen: 1723.24 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→10 Å
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Refine LS restraints |
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