+Open data
-Basic information
Entry | Database: PDB / ID: 1az5 | |||||||||
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Title | UNLIGANDED SIV PROTEASE STRUCTURE IN AN "OPEN" CONFORMATION | |||||||||
Components | SIV PROTEASE | |||||||||
Keywords | ASPARTYL PROTEASE / HIV / AIDS / PROTEINASE / ENDONUCLEASE | |||||||||
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 / structural molecule activity / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | |||||||||
Biological species | Simian immunodeficiency virus | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Rose, R.B. / Craik, C.S. / Stroud, R.M. | |||||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Domain flexibility in retroviral proteases: structural implications for drug resistant mutations. Authors: Rose, R.B. / Craik, C.S. / Stroud, R.M. #1: 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 | 1az5.cif.gz | 35.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1az5.ent.gz | 22.9 KB | Display | PDB format |
PDBx/mmJSON format | 1az5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/1az5 ftp://data.pdbj.org/pub/pdb/validation_reports/az/1az5 | HTTPS FTP |
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-Related structure data
Related structure data | 1samS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 10768.428 Da / Num. of mol.: 1 / Mutation: S4H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian immunodeficiency virus / Genus: Lentivirus / Strain: X90 / Gene: SIV(MAC)239 / Variant: 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: 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: 2.43 Å3/Da / Density % sol: 40 % | ||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: 100 MM SODIUM CACODYLATE, PH 6.5, 0.3 M NACL | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1994 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 7300 / % possible obs: 97 % / Redundancy: 5 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 |
Reflection shell | Resolution: 2→2.06 Å / % possible all: 94 |
Reflection shell | *PLUS % possible obs: 94 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SAM Resolution: 2→7 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 0 / Data cutoff low absF: 0 Isotropic thermal model: X-PLOR RESTRAINED INDIVID B-FACTORS σ(F): 0
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Displacement parameters | Biso mean: 23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.03 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 20
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.254 |