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Yorodumi- PDB-4heg: Crystal Structure of HIV-1 protease mutants R8Q complexed with in... -
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-Basic information
Entry | Database: PDB / ID: 4heg | ||||||
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Title | Crystal Structure of HIV-1 protease mutants R8Q complexed with inhibitor GRL-0519 | ||||||
Components | HIV-1 protease | ||||||
Keywords | HYDROLASE/Hydrolase Inhibitor / aspartic acid protease / drug resistance / HIV-1 protease inhibitor GRL-0519 / 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 type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Zhang, H. / Wang, Y.-F. / Weber, I.T. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Novel P2 tris-tetrahydrofuran group in antiviral compound 1 (GRL-0519) fills the S2 binding pocket of selected mutants of HIV-1 protease. Authors: Zhang, H. / Wang, Y.F. / Shen, C.H. / Agniswamy, J. / Rao, K.V. / Xu, C.X. / Ghosh, A.K. / Harrison, R.W. / Weber, I.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4heg.cif.gz | 106.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4heg.ent.gz | 82.5 KB | Display | PDB format |
PDBx/mmJSON format | 4heg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4heg_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4heg_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4heg_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 4heg_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/4heg ftp://data.pdbj.org/pub/pdb/validation_reports/he/4heg | HTTPS FTP |
-Related structure data
Related structure data | 4hdbC 4hdfC 4hdpC 4he9C 2nnkS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 10711.611 Da / Num. of mol.: 2 / Fragment: UNP residues 501-599 / Mutation: Q7K, R8Q, L33I, L63I, C67A, C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BRU/LAI / 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-G52 / ( | #3: 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: 2.7 Å3/Da / Density % sol: 54.51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 22%-24% saturated Ammonium Sulfate, 130-135 mM Sodium Phosphate, 0.05 M Sodium Citrate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, 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 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 27, 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: 1.46→50 Å / Num. all: 40949 / Num. obs: 40949 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.46→1.51 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3815 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2NNK Resolution: 1.46→10 Å / Num. parameters: 17369 / Num. restraintsaints: 23997 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
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Refine analyze | Num. disordered residues: 30 / Occupancy sum hydrogen: 1631 / Occupancy sum non hydrogen: 1720.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→10 Å
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Refine LS restraints |
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