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- PDB-4fl8: HIV-1 protease complexed with gem-diol-amine tetrahedral intermediate -
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Open data
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Basic information
Entry | Database: PDB / ID: 4fl8 | ||||||
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Title | HIV-1 protease complexed with gem-diol-amine tetrahedral intermediate | ||||||
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![]() | HYDROLASE / catalytic mechanism / drug resistance / aspartic 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 / 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 | ![]() ![]() ![]() | ||||||
![]() | Tie, Y.F. / Shen, C.H. / Weber, I.T. | ||||||
![]() | ![]() Title: Capturing the Reaction Pathway in Near-Atomic-Resolution Crystal Structures of HIV-1 Protease. Authors: Shen, C.H. / Tie, Y. / Yu, X. / Wang, Y.F. / Kovalevsky, A.Y. / Harrison, R.W. / Weber, I.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111 KB | Display | ![]() |
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PDB format | ![]() | 85.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.4 KB | Display | ![]() |
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Full document | ![]() | 476 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4flgC ![]() 4fm6C ![]() 3b7vS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 / Mutation: Q7K, L33I, L63I, C67A, C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Protein/peptide , 2 types, 2 molecules CD
#2: Protein/peptide | Mass: 800.983 Da / Num. of mol.: 1 / Fragment: see remark 999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#3: Protein/peptide | Mass: 895.009 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 3 types, 205 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | AUTHOR STATES THAT CHAIN C AND D ARE SELF PROTEOLYTIC PRODUCT OF HIV-1 PROTEASE. SEQUENCE OF CHAIN ...AUTHOR STATES THAT CHAIN C AND D ARE SELF PROTEOLYTI |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 0.1 M sodium acetate buffer and 0.41 M potassium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 6, 2007 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→50 Å / Num. all: 69949 / Num. obs: 66347 / % possible obs: 94.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3B7V Resolution: 1.2→10 Å / Num. parameters: 17800 / Num. restraintsaints: 23879 / 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: 41 / Occupancy sum hydrogen: 1634.31 / Occupancy sum non hydrogen: 1751.38 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→10 Å
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Refine LS restraints |
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