+Open data
-Basic information
Entry | Database: PDB / ID: 1yti | ||||||
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Title | SIV PROTEASE CRYSTALLIZED WITH PEPTIDE PRODUCT | ||||||
Components |
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Keywords | COMPLEX (HYDROLASE/PEPTIDE) / COMPLEX (HYDROLASE-PEPTIDE / ) AIDS / POLYPROTEIN / HYDROLASE / ASPARTYL PROTEASE / ENDONUCLEASE / RNA-DIRECTED DNA POLYMERASE / COMPLEX (HYDROLASE-PEPTIDE) COMPLEX | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / 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 ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / 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 / host cell cytoplasm / 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 / host cell nucleus / host cell plasma membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Simian immunodeficiency virus | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Rose, R.B. / Craik, C.S. / Douglas, N.L. / Stroud, R.M. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Three-dimensional structures of HIV-1 and SIV protease product complexes. Authors: Rose, R.B. / Craik, C.S. / Douglas, N.L. / Stroud, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yti.cif.gz | 32.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yti.ent.gz | 20.7 KB | Display | PDB format |
PDBx/mmJSON format | 1yti.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/1yti ftp://data.pdbj.org/pub/pdb/validation_reports/yt/1yti | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10768.428 Da / Num. of mol.: 1 / Mutation: CHAIN A, S4H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian immunodeficiency virus / Genus: Lentivirus / Strain: X90 / Description: PTAC-TAC / Gene: SIV(MAC)239 / Plasmid: PSOD-PR179 / Gene (production host): SIV(MAC)239 / Production host: Escherichia coli (E. coli) / References: UniProt: P05896, HIV-1 retropepsin |
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#2: Protein/peptide | Mass: 536.640 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 40 % | |||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 4900 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.053 |
Reflection | *PLUS Highest resolution: 2.2 Å |
Reflection shell | *PLUS % possible obs: 83 % |
-Processing
Software |
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Refinement | Resolution: 2.2→7 Å / σ(F): 0
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Displacement parameters | Biso mean: 29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_dihedral_angle_deg / Dev ideal: 27 |