+Open data
-Basic information
Entry | Database: PDB / ID: 3oua | ||||||
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Title | MDR769 HIV-1 protease complexed with p1/p6 hepta-peptide | ||||||
Components |
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Keywords | HYDROLASE/PEPTIDE / MDR HIV-1 protease / inhibitor / drug resistance / substrate envelope / HIV-1 protease / protease / p1/p6 substrate peptide / none / HYDROLASE / HYDROLASE-PEPTIDE complex | ||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / : / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase ...viral budding via host ESCRT complex / : / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral penetration into host nucleus / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / endonuclease activity / DNA recombination / host cell cytoplasm / 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 / cytoplasm Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 | 3oua.cif.gz | 58.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oua.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 3oua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/3oua ftp://data.pdbj.org/pub/pdb/validation_reports/ou/3oua | HTTPS FTP |
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-Related structure data
Related structure data | 3otsC 3otyC 3ou1C 3ou3C 3ou4C 3oubC 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 binds with p1/p6 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: 821.902 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: Q9YP46, 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: 2.36 Å3/Da / Density % sol: 47.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 0.8M NaCl 01 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: 1.6→45.6 Å / Num. all: 27395 / Num. obs: 27395 / % 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: 1.7→45.5 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.164 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R Free: 0.115 / 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: 24.962 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→45.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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