[English] 日本語
Yorodumi- PDB-4hdb: Crystal Structure of HIV-1 protease mutants D30N complexed with i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hdb | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of HIV-1 protease mutants D30N 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 / 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 type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Zhang, H. / Wang, Y.-F. / Shen, C.H. / Agniswamy, J. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4hdb.cif.gz | 107.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4hdb.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 4hdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hdb_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4hdb_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4hdb_validation.xml.gz | 13 KB | Display | |
Data in CIF | 4hdb_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/4hdb ftp://data.pdbj.org/pub/pdb/validation_reports/hd/4hdb | HTTPS FTP |
-Related structure data
Related structure data | 4hdfC 4hdpC 4he9C 4hegC 2qciS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 10739.691 Da / Num. of mol.: 2 / Fragment: UNP residues 501-599 / Mutation: Q7K, D30N, 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: Chemical | ChemComp-NA / | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.54 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.46 M NaCl and 0.1 M Sodium Citrate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: Aug 15, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→50 Å / Num. all: 37721 / Num. obs: 37721 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.49→1.54 Å / Redundancy: 2 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2189 / % possible all: 76.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2QCI Resolution: 1.49→10 Å / Num. parameters: 17063 / Num. restraintsaints: 23085 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 24 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1698.22 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.49→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|