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- PDB-4hdp: Crystal Structure of HIV-1 protease mutants I50V complexed with i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hdp | ||||||
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Title | Crystal Structure of HIV-1 protease mutants I50V complexed with inhibitor GRL-0519 | ||||||
![]() | HIV-1 Protease | ||||||
![]() | HYDROLASE/Hydrolase Inhibitor / aspartic acid protease / drug resistance / HIV-1 protease inhibitor GRL-0519 / HYDROLASE-Hydrolase Inhibitor complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shen, C.H. / Zhang, H. / Weber, I.T. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.2 KB | Display | ![]() |
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PDB format | ![]() | 83.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4hdbC ![]() 4hdfC ![]() 4he9C ![]() 4hegC ![]() 2f8gS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10726.649 Da / Num. of mol.: 2 / Fragment: UNP residues 501-599 / Mutation: Q7K, L33I, I50V, L63I, C67A, C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-G52 / ( | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.26-1.46 M NaCl, 0.06 M Sodium Acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.22→50 Å / Num. all: 64041 / Num. obs: 64041 / % possible obs: 91.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.22→1.26 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4497 / % possible all: 65.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2F8G Resolution: 1.22→10 Å / Num. parameters: 17455 / Num. restraintsaints: 22773 / 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: 20 / Occupancy sum hydrogen: 1637 / Occupancy sum non hydrogen: 1789.6 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.22→10 Å
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Refine LS restraints |
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