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Yorodumi- PDB-3dk1: Wild Type HIV-1 Protease with potent Antiviral inhibitor GRL-0105A -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dk1 | ||||||
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Title | Wild Type HIV-1 Protease with potent Antiviral inhibitor GRL-0105A | ||||||
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 / 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 type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å | ||||||
Authors | Wang, Y.F. / Weber, I.T. | ||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2008 Title: Potent HIV-1 protease inhibitors incorporating meso-bicyclic urethanes as P2-ligands: structure-based design, synthesis, biological evaluation and protein-ligand X-ray studies Authors: Ghosh, A.K. / Gemma, S. / Takayama, J. / Baldridge, A. / Leshchenko-Yashchuk, S. / Miller, H.B. / 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 | 3dk1.cif.gz | 110.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dk1.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 3dk1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/3dk1 ftp://data.pdbj.org/pub/pdb/validation_reports/dk/3dk1 | HTTPS FTP |
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-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 | ChemComp-NA / | #3: Chemical | #4: Chemical | ChemComp-G05 / ( | #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: 2.67 Å3/Da / Density % sol: 53.95 % |
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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, 1.5M sodium chloride. The inhibitor was ...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, 1.5M sodium chloride. 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: 1.07→50 Å / Num. all: 90315 / Num. obs: 90315 / % possible obs: 88.1 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.07→1.11 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.1 / % possible all: 51.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QCI Resolution: 1.07→10 Å / Num. parameters: 17628 / Num. restraintsaints: 24031 / 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 and Kretsinger, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 35 / Occupancy sum hydrogen: 1641 / Occupancy sum non hydrogen: 1714.89 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.07→10 Å
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Refine LS restraints |
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