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Open data
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Basic information
Entry | Database: PDB / ID: 3ndu | ||||||
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Title | HIV-1 Protease Saquinavir:Ritonavir 1:5 complex structure | ||||||
![]() | Protease | ||||||
![]() | hydrolase/hydrolase inhibitor / HIV-1 PROTEASE / HYDROLASE / AIDS / ASPARTYL PROTEASE / SAQUINAVIR / CARBAMYLATION / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | ![]() 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 / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Geremia, S. / Olajuyigbe, F.M. / Demitri, N. | ||||||
![]() | ![]() Title: Investigation of 2-Fold Disorder of Inhibitors and Relative Potency by Crystallizations of HIV-1 Protease in Ritonavir and Saquinavir Mixtures Authors: Olajuyigbe, F.M. / Demitri, N. / Geremia, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 201.4 KB | Display | ![]() |
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PDB format | ![]() | 160.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ndtC ![]() 3ndwC ![]() 3ndxC ![]() 3k4vS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 10767.702 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q7SSI0, UniProt: P03367*PLUS, HIV-1 retropepsin |
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-Non-polymers , 7 types, 285 molecules ![](data/chem/img/ROC.gif)
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![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
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![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
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![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-DMS / #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-CL / #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 43.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: AMMONIUM SULFATE, DMSO, SODIUM CITRATE, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2008 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→10 Å / Num. all: 95332 / Num. obs: 70768 / % possible obs: 93.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3K4V Resolution: 1.25→10 Å / Num. parameters: 34311 / Num. restraintsaints: 46294 / Cross valid method: FREE R / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 62 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3452.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→10 Å
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Refine LS restraints |
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