[English] 日本語
Yorodumi- PDB-5bry: HIV-1 wild Type protease with GRL-011-11A (a methylamine bis-Tetr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bry | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | HIV-1 wild Type protease with GRL-011-11A (a methylamine bis-Tetrahydrofuran P2-Ligand, sulfonamide isostere derivate) | ||||||||||||||||||||||||
Components | Protease | ||||||||||||||||||||||||
Keywords | HYDROLASE/HYDROLASE Inhibitor / 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 / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 BH10 | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||||||||||||||||||||
Authors | Wang, Y.-F. / Agniswamy, J. / Weber, I.T. | ||||||||||||||||||||||||
Funding support | United States, Japan, 7items
| ||||||||||||||||||||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Design of HIV-1 Protease Inhibitors with Amino-bis-tetrahydrofuran Derivatives as P2-Ligands to Enhance Backbone-Binding Interactions: Synthesis, Biological Evaluation, and Protein-Ligand X-ray Studies. Authors: Ghosh, A.K. / Martyr, C.D. / Osswald, H.L. / Sheri, V.R. / Kassekert, L.A. / Chen, S. / Agniswamy, J. / Wang, Y.F. / Hayashi, H. / Aoki, M. / Weber, I.T. / Mitsuya, H. | ||||||||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5bry.cif.gz | 108.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5bry.ent.gz | 81.3 KB | Display | PDB format |
PDBx/mmJSON format | 5bry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/5bry ftp://data.pdbj.org/pub/pdb/validation_reports/br/5bry | HTTPS FTP |
---|
-Related structure data
Related structure data | 5bs4C 3nu3S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 type 1 BH10 Strain: isolate BH10 / Gene: gag-pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03366, HIV-1 retropepsin #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-4UY / ( | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.4 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 1.4 M NaCl, 0.1 M sodium Acetate, pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 28, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→50 Å / Num. all: 49960 / Num. obs: 49960 / % possible obs: 94.3 % / Redundancy: 6 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 1.34→1.39 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.1 / % possible all: 59.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NU3 Resolution: 1.34→50 Å / Num. parameters: 16719 / Num. restraintsaints: 22504 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 37 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1673 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.34→50 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|