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Yorodumi- PDB-4fl8: HIV-1 protease complexed with gem-diol-amine tetrahedral intermediate -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fl8 | ||||||
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Title | HIV-1 protease complexed with gem-diol-amine tetrahedral intermediate | ||||||
Components |
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Keywords | HYDROLASE / catalytic mechanism / drug resistance / aspartic protease | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / 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 Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Tie, Y.F. / Shen, C.H. / Weber, I.T. | ||||||
Citation | Journal: Biochemistry / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fl8.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fl8.ent.gz | 85.1 KB | Display | PDB format |
PDBx/mmJSON format | 4fl8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/4fl8 ftp://data.pdbj.org/pub/pdb/validation_reports/fl/4fl8 | HTTPS FTP |
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-Related structure data
Related structure data | 4flgC 4fm6C 3b7vS S: Starting model for refinement 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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-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.) Human immunodeficiency virus 1 / Gene: gag-pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03367, HIV-1 retropepsin |
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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.) Human immunodeficiency virus 1 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03367*PLUS |
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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.) Human immunodeficiency virus 1 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03367*PLUS |
-Non-polymers , 3 types, 205 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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