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Yorodumi- PDB-3qbf: HIV-1 protease (mutant Q7K L33I L63I) in complex with a three-arm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qbf | ||||||
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Title | HIV-1 protease (mutant Q7K L33I L63I) in complex with a three-armed pyrrolidine-based inhibitor | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Aspartyl Protease / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Lindemann, I. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: To be Published Title: Design of a series of novel three-armed pyrrolidine-based inhibitors for HIV-1 protease Authors: Lindemann, I. / Klee, N. / Heine, A. / Diederich, W.E. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qbf.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qbf.ent.gz | 42.9 KB | Display | PDB format |
PDBx/mmJSON format | 3qbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qbf_validation.pdf.gz | 819.7 KB | Display | wwPDB validaton report |
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Full document | 3qbf_full_validation.pdf.gz | 821.7 KB | Display | |
Data in XML | 3qbf_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 3qbf_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/3qbf ftp://data.pdbj.org/pub/pdb/validation_reports/qb/3qbf | HTTPS FTP |
-Related structure data
Related structure data | 3qpjC 3qrmC 3qroC 3qrsC 2pqzS S: Starting model for refinement C: citing same article (ref.) |
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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: 10804.808 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 (BRU ISOLATE) Plasmid: pET24a / Production host: Escherichia coli (E. coli) / References: UniProt: P03367, HIV-1 retropepsin #2: Chemical | ChemComp-JHG / | #3: Chemical | #4: Chemical | #5: 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: 2.7 Å3/Da / Density % sol: 54.38 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 700mM NaCl, 0.1M Na citrate, 100mM DTT, 3mM NaN3, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 24, 2010 / Details: mirrors |
Radiation | Monochromator: Double Crystal Monochromator KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→30 Å / Num. all: 41616 / Num. obs: 41616 / % possible obs: 100 % / Redundancy: 4.5 % / Biso Wilson estimate: 12.74 Å2 / Rsym value: 0.062 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 1989 / Rsym value: 0.286 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PQZ Resolution: 1.45→27.569 Å / Occupancy max: 1 / Occupancy min: 0.28 / SU ML: 0.18 / σ(F): 0 / Phase error: 17.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.032 Å2 / ksol: 0.398 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.37 Å2 / Biso mean: 16.2572 Å2 / Biso min: 5.05 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→27.569 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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