+Open data
-Basic information
Entry | Database: PDB / ID: 3oub | ||||||
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Title | MDR769 HIV-1 protease complexed with NC/p1 hepta-peptide | ||||||
Components |
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Keywords | HYDROLASE/PEPTIDE / MDR HIV-1 protease / inhibitor / drug resistance / substrate envelope / HIV-1 protease / protease / NC/p1 substrate peptide / none / HYDROLASE / HYDROLASE-PEPTIDE 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 / 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 / endonuclease activity / DNA recombination / nucleic acid binding / 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 | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Liu, Z. / Wang, Y. / Brunzelle, J. / Kovari, I.A. / Kovari, L.C. | ||||||
Citation | Journal: Protein J. / Year: 2011 Title: Nine Crystal Structures Determine the Substrate Envelope of the MDR HIV-1 Protease. Authors: Liu, Z. / Wang, Y. / Brunzelle, J. / Kovari, I.A. / Kovari, L.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oub.cif.gz | 58 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oub.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 3oub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oub_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 3oub_full_validation.pdf.gz | 443.1 KB | Display | |
Data in XML | 3oub_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 3oub_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/3oub ftp://data.pdbj.org/pub/pdb/validation_reports/ou/3oub | HTTPS FTP |
-Related structure data
Related structure data | 3otsC 3otyC 3ou1C 3ou3C 3ou4C 3ouaC 3oucC 3oudC 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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Unit cell |
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Details | MDR HIV-1 protease dimer binds with NC/p1 substrate peptide |
-Components
#1: Protein | Mass: 10769.635 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: Q000H7, UniProt: P35963*PLUS #2: Protein/peptide | | Mass: 805.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in HIV-1 / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9DZ78, UniProt: P35963*PLUS #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: 2.37 Å3/Da / Density % sol: 48.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 0.8M NaCl 0.1 M MES , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 173 K | ||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0332 Å | ||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 9, 2008 | ||||||||||||||||||||||
Radiation | Monochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | ||||||||||||||||||||||
Reflection | Resolution: 1.4→27.26 Å / Num. all: 40904 / Num. obs: 40904 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 | ||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→34 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 1.736 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.103 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.419 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.602→1.643 Å / Total num. of bins used: 20
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