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Yorodumi- PDB-5jg1: HIV-1 wild Type protease with GRL-031-14A (a Adamantane P1-Ligand... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jg1 | ||||||||||||||||||||||||
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Title | HIV-1 wild Type protease with GRL-031-14A (a Adamantane P1-Ligand with tetrahydropyrano-tetrahydrofuran in P2 and isobutylamine in P1') | ||||||||||||||||||||||||
Components | Protease | ||||||||||||||||||||||||
Keywords | hydrolase/hydrolase inhibitor / Adamantane / HIV-1 protease inhibitor GRL-031-14A / darunavir / multidrug-resistant / hydrolase-hydrolase inhibitor complex | ||||||||||||||||||||||||
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 / Resolution: 1.16 Å | ||||||||||||||||||||||||
Authors | Wang, Y.-F. / Agniswamy, J. / Weber, I.T. | ||||||||||||||||||||||||
Funding support | United States, Japan, 7items
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Citation | Journal: J.Med.Chem. / Year: 2016 Title: Probing Lipophilic Adamantyl Group as the P1-Ligand for HIV-1 Protease Inhibitors: Design, Synthesis, Protein X-ray Structural Studies, and Biological Evaluation. Authors: Ghosh, A.K. / Osswald, H.L. / Glauninger, K. / Agniswamy, J. / Wang, Y.F. / Hayashi, H. / Aoki, M. / 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 | 5jg1.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jg1.ent.gz | 77.7 KB | Display | PDB format |
PDBx/mmJSON format | 5jg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jg1_validation.pdf.gz | 765.8 KB | Display | wwPDB validaton report |
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Full document | 5jg1_full_validation.pdf.gz | 767.2 KB | Display | |
Data in XML | 5jg1_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 5jg1_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/5jg1 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/5jg1 | HTTPS FTP |
-Related structure data
Related structure data | 5jfpC 5jfuC 3nu3S 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 , 1 types, 2 molecules AB
#1: Protein | Mass: 10740.677 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I, C67A, 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: C8B467, UniProt: P03366*PLUS |
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-Non-polymers , 5 types, 189 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-6KR / ( | #6: 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: 54.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.25 M NaCl, 0.1M Acetate, pH 5.5 / PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→50 Å / Num. obs: 77803 / % possible obs: 94.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 9.8 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.16→1.2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2 / % possible all: 64.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NU3 Resolution: 1.16→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0 Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 19 / Occupancy sum hydrogen: 1651 / Occupancy sum non hydrogen: 1722.9 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.16→50 Å
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Refine LS restraints |
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