+Open data
-Basic information
Entry | Database: PDB / ID: 4flg | ||||||
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Title | HIV-1 protease mutant I47V complexed with reaction intermediate | ||||||
Components |
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Keywords | HYDROLASE / catalytic mechanism / drug resistance / aspartic protease | ||||||
Function / homology | Function and homology information RNA stem-loop binding / host cell / 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 ...RNA stem-loop binding / host cell / 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 / 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 / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.31 Å | ||||||
Authors | Yu, X. / 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 | 4flg.cif.gz | 104.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4flg.ent.gz | 80 KB | Display | PDB format |
PDBx/mmJSON format | 4flg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/4flg ftp://data.pdbj.org/pub/pdb/validation_reports/fl/4flg | HTTPS FTP |
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-Related structure data
Related structure data | 4fl8C 4fm6C 1fg6S C: citing same article (ref.) S: Starting model for refinement |
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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 BA
#1: Protein | Mass: 10726.649 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, I47V, L63I, C67A, C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03367, HIV-1 retropepsin |
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-HIV-1 protease, ... , 3 types, 3 molecules CEF
#2: Protein/peptide | Mass: 487.547 Da / Num. of mol.: 1 / Fragment: see remark 999 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 |
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#3: Protein/peptide | Mass: 372.460 Da / Num. of mol.: 1 / Fragment: see remark 999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03367 |
#4: Protein/peptide | Mass: 373.445 Da / Num. of mol.: 1 / Fragment: see remark 999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03367 |
-Non-polymers , 6 types, 193 molecules
#5: Chemical | ChemComp-GLU / | ||||
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#6: Chemical | ChemComp-ILE / | ||||
#7: Chemical | ChemComp-NA / | ||||
#8: Chemical | ChemComp-CL / #9: Chemical | #10: Water | ChemComp-HOH / | |
-Details
Sequence details | AUTHOR STATES THAT CHAIN C, E AND F ARE SELF PROTEOLYTIC PRODUCT OF HIV-1 PROTEASE. SEQUENCE OF ...AUTHOR STATES THAT CHAIN C, E AND F 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: 2.53 Å3/Da / Density % sol: 51.34 % |
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Crystal grow | Temperature: 298 K / pH: 5 Details: 0.05 M sodium acetate buffer, 1.2 M sodium formate, and 2.5% PEG8000, pH 5.0, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 16, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.31→50 Å / Num. all: 56095 / Num. obs: 53227 / % possible obs: 98.8 % / 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: AB INITIO PHASING Starting model: 1FG6 Resolution: 1.31→10 Å / Num. parameters: 16870 / Num. restraintsaints: 21928 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: NO CUTOFF FOR ANISOTROPIC REFINEMENT
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Refine analyze | Num. disordered residues: 25 / Occupancy sum hydrogen: 1641.88 / Occupancy sum non hydrogen: 1732.4 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.31→10 Å
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Refine LS restraints |
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