+Open data
-Basic information
Entry | Database: PDB / ID: 3ndx | ||||||
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Title | HIV-1 Protease Saquinavir:Ritonavir 1:50 complex structure | ||||||
Components | Protease | ||||||
Keywords | hydrolase/hydrolase inhibitor / HIV-1 PROTEASE / HYDROLASE / AIDS / ASPARTYL PROTEASE / SAQUINAVIR / 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 / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / 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 / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.03 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 | 3ndx.cif.gz | 112.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ndx.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 3ndx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/3ndx ftp://data.pdbj.org/pub/pdb/validation_reports/nd/3ndx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10740.677 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) References: UniProt: Q7SSI0, UniProt: P03367*PLUS, HIV-1 retropepsin |
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-Non-polymers , 6 types, 266 molecules
#2: Chemical | ChemComp-RIT / | ||||||||
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#3: Chemical | ChemComp-DMS / #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.31 % |
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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 | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 1.03→10 Å / Num. all: 82398 / Num. obs: 71030 / % possible obs: 90.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: NONE Resolution: 1.03→10 Å / Num. parameters: 18490 / Num. restraintsaints: 24561 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 61 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1853.76 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.03→10 Å
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Refine LS restraints |
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