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Yorodumi- PDB-1ida: CRYSTAL STRUCTURES OF HIV-2 PROTEASE IN COMPLEX WITH INHIBITORS C... -
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-Basic information
Entry | Database: PDB / ID: 1ida | ||||||
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Title | CRYSTAL STRUCTURES OF HIV-2 PROTEASE IN COMPLEX WITH INHIBITORS CONTAINING THE HYDROXYETHYLAMINE DIPEPTIDE ISOSTERE | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / AIDS / Protease / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information HIV-2 retropepsin / 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 ...HIV-2 retropepsin / 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 / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / 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 / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 2 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | ||||||
Authors | Tong, L. / Anderson, P.C. | ||||||
Citation | Journal: Structure / Year: 1995 Title: Crystal structures of HIV-2 protease in complex with inhibitors containing the hydroxyethylamine dipeptide isostere. Authors: Tong, L. / Pav, S. / Mui, S. / Lamarre, D. / Yoakim, C. / Beaulieu, P. / Anderson, P.C. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 Title: Crystal Structure of Human Immunodeficiency Virus (HIV) Type 2 Protease in Complex with a Reduced Amide Inhibitor and Comparison with HIV-1 Protease Structures Authors: Tong, L. / Pav, S. / Pargellis, C. / Do, F. / Lamarre, D. / Anderson, P.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ida.cif.gz | 52.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ida.ent.gz | 38.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ida.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/1ida ftp://data.pdbj.org/pub/pdb/validation_reports/id/1ida | 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
#1: Protein | Mass: 10728.337 Da / Num. of mol.: 2 / Fragment: rsidues 514-622 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 2 / Genus: Lentivirus / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P04584, HIV-2 retropepsin #2: Chemical | ChemComp-0PO / | Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 724.954 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H52N6O4S References: N-[(1R)-1-{[(1S,2S)-1-benzyl-3-{(2R,4S)-2-(tert-butylcarbamoyl)-4-[(pyridin-3-ylmethyl)sulfanyl]piperidin-1-yl}- 2-hydroxypropyl]carbamoyl}-2-methylpropyl]quinoline-2-carboxamide #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.45 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Num. obs: 22017 / % possible obs: 80 % / Observed criterion σ(F): 2 |
-Processing
Software |
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Refinement | Resolution: 1.7→6 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 1.7→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.196 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.6 |