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- PDB-3oqa: Crystal Structures of Multidrug-Resistant Clinical Isolate 769 HI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3oqa | ||||||
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Title | Crystal Structures of Multidrug-Resistant Clinical Isolate 769 HIV-1 Protease Variants | ||||||
![]() | HIV-1 Protease | ||||||
![]() | HYDROLASE / Protease | ||||||
Function / homology | ![]() 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 / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Yedidi, R.S. / Proteasa, G. / Martinez-Cajas, J.L. / Vickrey, J.F. / Martin, P.D. / Wawrzak, Z. / Kovari, L.C. | ||||||
![]() | ![]() Title: Contribution of the 80s loop of HIV-1 protease to the multidrug-resistance mechanism: crystallographic study of MDR769 HIV-1 protease variants. Authors: Yedidi, R.S. / Proteasa, G. / Martinez, J.L. / Vickrey, J.F. / Martin, P.D. / Wawrzak, Z. / Liu, Z. / Kovari, I.A. / Kovari, L.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 32.4 KB | Display | ![]() |
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PDB format | ![]() | 21.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.8 KB | Display | ![]() |
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Full document | ![]() | 427.8 KB | Display | |
Data in XML | ![]() | 6.7 KB | Display | |
Data in CIF | ![]() | 8.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3oq7C ![]() 3oqdC ![]() 3pj6C ![]() 1tw7S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10755.608 Da / Num. of mol.: 1 / Fragment: UNP residues 1-99 / Mutation: T82S Source method: isolated from a genetically manipulated source Details: Multidrug-resistant clinical isolate # 769 HIV-1 protease Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.42 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.3-1.0M sodium chloride in the pH range 5.5-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 22, 2004 / Details: HighRes2 mirror system |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→27.28 Å / Num. obs: 5466 / Redundancy: 6.4 % / Rsym value: 0.071 |
Reflection shell | Highest resolution: 2.25 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 764 / Rsym value: 0.371 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TW7 Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.845 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 28.434 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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