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Yorodumi- PDB-3b80: HIV-1 protease mutant I54V complexed with gem-diol-amine intermed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b80 | ||||||
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Title | HIV-1 protease mutant I54V complexed with gem-diol-amine intermediate NLLTQI | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE SUBSTRATE COMPLEX / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 / identical protein binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 BH10 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.5 Å | ||||||
Authors | Chumanevich, A.A. / Kovalevsky, A.Y. / Weber, I.T. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Caught in the Act: The 1.5 A Resolution Crystal Structures of the HIV-1 Protease and the I54V Mutant Reveal a Tetrahedral Reaction Intermediate. Authors: Kovalevsky, A.Y. / Chumanevich, A.A. / Liu, F. / Louis, J.M. / 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 | 3b80.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b80.ent.gz | 79.1 KB | Display | PDB format |
PDBx/mmJSON format | 3b80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/3b80 ftp://data.pdbj.org/pub/pdb/validation_reports/b8/3b80 | HTTPS FTP |
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-Related structure data
Related structure data | 3b7vC 2ienS 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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Details | The authors state that the biological assembly is composed of the HIV-1 protease dimer, complexed with its substrate, the gem-diol-amine tetrahedral intermediate peptide NLLTQI |
-Components
#1: Protein | Mass: 10726.649 Da / Num. of mol.: 2 / Fragment: UNP residues 501-599 / Mutation: Q507K, L533I, I554V, L563I, C567A, C595A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 BH10 Genus: Lentivirus / Species: Human immunodeficiency virus 1Subtypes of HIV / Strain: BH5 ISOLATE / Gene: gag-pol / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P04587, UniProt: Q7SSI0*PLUS, HIV-1 retropepsin #2: Protein/peptide | | Type: Peptide-like / Class: Inhibitor / Mass: 718.839 Da / Num. of mol.: 1 / Fragment: self proteolytic product of HIV-1 protease Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 BH10 Genus: Lentivirus / Species: Human immunodeficiency virus 1Subtypes of HIV / Strain: BH5 ISOLATE / Gene: gag-pol / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: PDB-3B7V, N-{(2S)-2-[(L-asparaginyl-L-leucyl)amino]-1,1-dihydroxy-4-methylpentyl}-L-threonyl-L-glutaminyl-L-isoleucine #3: Chemical | ChemComp-NA / | #4: Chemical | #5: 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: 2.63 Å3/Da / Density % sol: 53.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 12.5mM sodium phosphate/50mM sodium citrate buffer, 8% NaCl (w/w), 10% glycerol (v/v), pH 6.0, 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: 0.8 / Wavelength: 0.8 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 12, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 37411 / Num. obs: 30352 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.064 |
Reflection shell | Resolution: 1.5→1.55 Å / % possible all: 85.8 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: PDB entry 2IEN Resolution: 1.5→10 Å / Num. parameters: 16270 / Num. restraintsaints: 20502 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
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Refine analyze | Num. disordered residues: 13 / Occupancy sum hydrogen: 1614 / Occupancy sum non hydrogen: 1724.1 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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