+Open data
-Basic information
Entry | Database: PDB / ID: 3bgb | ||||||
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Title | HIV-1 protease in complex with a isobutyl decorated oligoamine | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE / protein-ligand complex / AIDS / Aspartyl protease / Capsid maturation / Core protein / Cytoplasm / DNA integration / DNA recombination / DNA-directed DNA polymerase / Endonuclease / Lipoprotein / Magnesium / Membrane / Metal-binding / Multifunctional enzyme / Myristate / Nuclease / Nucleotidyltransferase / Nucleus / Phosphoprotein / Protease / RNA-binding / RNA-directed DNA polymerase / Transferase / Viral nucleoprotein / Virion / Zinc / Zinc-finger | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / viral translational frameshifting / 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 1 | ||||||
Method | X-RAY DIFFRACTION / AB INITIO / Resolution: 1.9 Å | ||||||
Authors | Boettcher, J. / Blum, A. / Sammet, B. / Heine, A. / Diederich, W.E. / Klebe, G. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2008 Title: Achiral oligoamines as versatile tool for the development of aspartic protease inhibitors Authors: Blum, A. / Sammet, B. / Luksch, T. / Heine, A. / Klebe, G. / Diederich, W.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bgb.cif.gz | 54.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bgb.ent.gz | 38 KB | Display | PDB format |
PDBx/mmJSON format | 3bgb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bgb_validation.pdf.gz | 784.1 KB | Display | wwPDB validaton report |
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Full document | 3bgb_full_validation.pdf.gz | 787.1 KB | Display | |
Data in XML | 3bgb_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 3bgb_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/3bgb ftp://data.pdbj.org/pub/pdb/validation_reports/bg/3bgb | HTTPS FTP |
-Related structure data
Related structure data | 3bgcC 2pqzS C: citing same article (ref.) 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
#1: Protein | Mass: 10803.756 Da / Num. of mol.: 2 / Fragment: UNP residues 501-599 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Gene: gag-pol / Plasmid: peT11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(d3)pLysS References: UniProt: P03367, UniProt: P04587*PLUS, HIV-1 retropepsin #2: Chemical | ChemComp-LJG / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.68 Å3/Da / Density % sol: 54.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 3.0M NaCl, 0.1M Bist-Tris, pH6.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 18795 / Num. obs: 18795 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.6 / Num. unique all: 940 / Rsym value: 0.49 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: PDB ENTRY 2PQZ Resolution: 1.9→25 Å / Num. parameters: 6671 / Num. restraintsaints: 6295 / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 1580 / Occupancy sum non hydrogen: 1664 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→25 Å
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Refine LS restraints |
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