+Open data
-Basic information
Entry | Database: PDB / ID: 3ndt | ||||||
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Title | HIV-1 Protease Saquinavir:Ritonavir 1:1 complex structure | ||||||
Components | Protease | ||||||
Keywords | hydrolase/hydrolase inhibitor / HYDROLASE / AIDS / ASPARTYL PROTEASE / CARBAMYLATION / 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 ...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-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 BH10 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Geremia, S. / Olajuyigbe, F.M. / Demitri, N. | ||||||
Citation | Journal: Cryst.Growth Des. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ndt.cif.gz | 186.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ndt.ent.gz | 149.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ndt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/3ndt ftp://data.pdbj.org/pub/pdb/validation_reports/nd/3ndt | HTTPS FTP |
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-Related structure data
Related structure data | 3nduC 3ndwC 3ndxC 3k4vS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Human immunodeficiency virus type 1 BH10 Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, HIV-1 retropepsin |
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-Non-polymers , 5 types, 150 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-DMS / #5: Chemical | #6: 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: 2.19 Å3/Da / Density % sol: 43.81 % |
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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: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å |
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: 1.72→5 Å / Num. all: 34735 / Num. obs: 24746 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3K4V Resolution: 1.72→5 Å / Num. parameters: 31477 / Num. restraintsaints: 41831 / Cross valid method: FREE R / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 29 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3287.75 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→5 Å
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Refine LS restraints |
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