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Yorodumi- PDB-5ult: HIV-1 wild Type protease with GRL-100-13A (a Crown-like Oxotricyc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ult | |||||||||||||||||||||||||||
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Title | HIV-1 wild Type protease with GRL-100-13A (a Crown-like Oxotricyclic Core as the P2-Ligand with the sulfonamide isostere as the P2' group) | |||||||||||||||||||||||||||
Components | Protease | |||||||||||||||||||||||||||
Keywords | hydrolase/hydrolase inhibitor / Crown-like Oxotricyclic Core / HIV-1 protease inhibitor GRL-100-13A / darunavir / multidrug-resistant / hydrolase inhibitor complex / hydrolase-hydrolase inhibitor complex | |||||||||||||||||||||||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / viral translational frameshifting / 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: 1.53 Å | |||||||||||||||||||||||||||
Authors | Wang, Y.-F. / Agniswamy, J. / Weber, I.T. | |||||||||||||||||||||||||||
Funding support | United States, Japan, 8items
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Citation | Journal: J. Med. Chem. / Year: 2017 Title: Design and Development of Highly Potent HIV-1 Protease Inhibitors with a Crown-Like Oxotricyclic Core as the P2-Ligand To Combat Multidrug-Resistant HIV Variants. Authors: Ghosh, A.K. / Rao, K.V. / Nyalapatla, P.R. / Osswald, H.L. / Martyr, C.D. / Aoki, M. / Hayashi, H. / Agniswamy, J. / Wang, Y.F. / Bulut, H. / Das, D. / 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 | 5ult.cif.gz | 103 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ult.ent.gz | 77.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ult.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ult_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5ult_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5ult_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 5ult_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/5ult ftp://data.pdbj.org/pub/pdb/validation_reports/ul/5ult | HTTPS FTP |
-Related structure data
Related structure data | 3nu3S 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 / 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 #2: Chemical | ChemComp-NA / | #3: Chemical | #4: Chemical | ChemComp-8FM / ( | #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: 2.71 Å3/Da / Density % sol: 54.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 1.3 M NaCl, 0.1 M Sodium Acetate, pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 19, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50 Å / Num. obs: 35003 / % possible obs: 97.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.53→1.58 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 3.3 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NU3 Resolution: 1.53→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: 23 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1640.25 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→50 Å
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Refine LS restraints |
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