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Yorodumi- PDB-1vij: HIV-1 PROTEASE COMPLEXED WITH THE INHIBITOR HOE/BAY 793 HEXAGONAL FORM -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vij | ||||||
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Title | HIV-1 PROTEASE COMPLEXED WITH THE INHIBITOR HOE/BAY 793 HEXAGONAL FORM | ||||||
Components | HIV-1 PROTEASE | ||||||
Keywords | ASPARTYL PROTEASE / HUMAN IMMUNODEFICIENCY VIRUS / HOE/BAY 793: INHIBITOR DESIGN | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / 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 / 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 / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | ||||||
Authors | Lange-Savage, G. / Berchtold, H. / Liesum, A. / Hilgenfeld, R. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 1997 Title: Structure of HOE/BAY 793 complexed to human immunodeficiency virus (HIV-1) protease in two different crystal forms--structure/function relationship and influence of crystal packing. Authors: Lange-Savage, G. / Berchtold, H. / Liesum, A. / Budt, K.H. / Peyman, A. / Knolle, J. / Sedlacek, J. / Fabry, M. / Hilgenfeld, R. #1: Journal: Eur.J.Biochem. / Year: 1997 Title: Erratum. Structure of Hoe/Bay 793 Complexed to Human Immunodeficiency Virus (HIV-1) Protease in Two Different Crystal Forms--Structure/Function Relationship and Influence of Crystal Packing Authors: Lange-Savage, G. / Berchtold, H. / Liesum, A. / Budt, K.H. / Peyman, A. / Knolle, J. / Sedlacek, J. / Fabry, M. / Hilgenfeld, R. #2: Journal: Annu.Rev.Biochem. / Year: 1993 Title: Structure-Based Inhibitors of HIV-1 Protease Authors: Wlodawer, A. / Erickson, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vij.cif.gz | 55.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vij.ent.gz | 39.6 KB | Display | PDB format |
PDBx/mmJSON format | 1vij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/1vij ftp://data.pdbj.org/pub/pdb/validation_reports/vi/1vij | 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: 10830.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P12499, HIV-1 retropepsin #2: Chemical | ChemComp-BAY / | #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: 2.28 Å3/Da / Density % sol: 46.08 % | ||||||||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 37 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.8 / 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 Highest resolution: 2.4 Å / Num. obs: 5468 / % possible obs: 90 % / Num. measured all: 18894 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å / % possible obs: 93 % |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.4→8 Å / σ(F): 0 Details: RMS DEVIATIONS FROM IDEAL VALUES ANGLE DISTANCE (DEGREES) : 4.40
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Displacement parameters | Biso mean: 24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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Refine LS restraints | *PLUS Type: p_plane_restr / Dev ideal: 0.016 |