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Yorodumi- PDB-3b7v: HIV-1 protease complexed with gem-diol-amine tetrahedral intermed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b7v | ||||||
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Title | HIV-1 protease complexed with gem-diol-amine tetrahedral intermediate NLLTQI | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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 / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 BH10 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.46 Å | ||||||
Authors | Kovalevsky, A.Y. / Chumanevich, A.A. / 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 | 3b7v.cif.gz | 105.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b7v.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 3b7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b7v_validation.pdf.gz | 459.2 KB | Display | wwPDB validaton report |
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Full document | 3b7v_full_validation.pdf.gz | 463.2 KB | Display | |
Data in XML | 3b7v_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 3b7v_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/3b7v ftp://data.pdbj.org/pub/pdb/validation_reports/b7/3b7v | HTTPS FTP |
-Related structure data
Related structure data | 3b80C 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
-Protein / Protein/peptide , 2 types, 3 molecules ABC
-Non-polymers , 4 types, 177 molecules
#3: Chemical | ChemComp-NA / | ||||
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#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 50mM sodium phosphate/100mM sodium citrate, 10% NaCl (w/w), 2.5% 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: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→50 Å / Num. all: 40494 / Num. obs: 32850 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.103 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: PDB entry 2IEN Resolution: 1.46→10 Å / Num. parameters: 16443 / Num. restraintsaints: 20980 / 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: 18 / Occupancy sum hydrogen: 1618 / Occupancy sum non hydrogen: 1715.2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→10 Å
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Refine LS restraints |
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