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Yorodumi- PDB-1bai: Crystal structure of Rous sarcoma virus protease in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bai | ||||||
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Title | Crystal structure of Rous sarcoma virus protease in complex with inhibitor | ||||||
Components | PROTEASE | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / PROTEIN-MEDIATED INTERACTION / VIRAL MATURATION / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information reverse transcription / host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...reverse transcription / host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / viral capsid / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / nucleic acid binding / structural constituent of virion / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Rous sarcoma virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Wu, J. / Adomat, J.M. / Ridky, T.W. / Louis, J.M. / Leis, J. / Harrison, R.W. / Weber, I.T. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Structural basis for specificity of retroviral proteases. Authors: Wu, J. / Adomat, J.M. / Ridky, T.W. / Louis, J.M. / Leis, J. / 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 | 1bai.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bai.ent.gz | 56.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bai_validation.pdf.gz | 464.6 KB | Display | wwPDB validaton report |
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Full document | 1bai_full_validation.pdf.gz | 479.9 KB | Display | |
Data in XML | 1bai_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 1bai_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/1bai ftp://data.pdbj.org/pub/pdb/validation_reports/ba/1bai | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13648.806 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rous sarcoma virus / References: UniProt: O92805, UniProt: P03322*PLUS #2: Chemical | ChemComp-0Q4 / | Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 833.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H70N11O8 / Details: PURIFIED FROM THE INCLUSION BODY FRACTION References: N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl- L-alanyl-L-norleucinamide #3: Water | ChemComp-HOH / | Nonpolymer details | PEPTIDE INHIBITOR 0Q4 HAS A REDUCED PEPTIDE (-CH2-NH) INSTEAD OF THE NORMAL PEPTIDE LINK (-CO-NH). | |
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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: 2.66 Å3/Da / Density % sol: 53.67 % | ||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Aug 15, 1996 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→8 Å / Num. obs: 9601 / % possible obs: 76.8 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.0943 / Rsym value: 0.175 |
Reflection shell | Resolution: 2.4→2.51 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 2
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Displacement parameters | Biso mean: 18.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.51 Å / Total num. of bins used: 8 /
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.175 / Rfactor Rfree: 0.293 / Rfactor Rwork: 0.175 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.244 / Num. reflection Rfree: 98 / Rfactor Rwork: 0.175 |