+Open data
-Basic information
Entry | Database: PDB / ID: 2qmp | ||||||
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Title | Crystal Structure of HIV-1 protease complexed with PL-100 | ||||||
Components | Pol polyprotein | ||||||
Keywords | HYDROLASE / HIV-1 protease / Aspartyl protease / Multifunctional enzyme / Nucleotidyltransferase / RNA-directed DNA polymerase / Transferase | ||||||
Function / homology | Function and homology information viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / endonuclease activity / aspartic-type endopeptidase activity / proteolysis / DNA binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Allison, T.J. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of HIV-1 protease complexed with PL-100 Authors: Coburn, C.A. / Allison, T.J. / Holloway, M.K. / Wu, J.J. / Wainberg, M.A. / Vacca, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qmp.cif.gz | 57.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qmp.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 2qmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/2qmp ftp://data.pdbj.org/pub/pdb/validation_reports/qm/2qmp | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10830.781 Da / Num. of mol.: 2 / Fragment: protease domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WFL7, HIV-1 retropepsin #2: Chemical | #3: 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: 2.65 Å3/Da / Density % sol: 53.56 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1:1 protein:reservoir, 6 mg/mL protein, 0.6 mM PL-100, protein buffer: 10 mM MES, 1 mM DTT, 1 mM EDTA, 3 mM NaN3, reservoir: 0.6 M NaCl, 100 mM NaOAc, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 93 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 11, 2006 / Details: Osmic VariMax HR | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→47.96 Å / Num. obs: 21909 / % possible obs: 99.6 % / Redundancy: 4.38 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 1.8→47.96 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.908 / SU B: 2.955 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.741 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→47.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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