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Yorodumi- PDB-2pk6: Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I) in Complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pk6 | ||||||
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Title | Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I) in Complex with KNI-10033 | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / PROTEASE COMPLEX / Viral Protein / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Armstrong, A.A. / Lafont, V. / Kiso, Y. / Freire, E. / Amzel, L.M. | ||||||
Citation | Journal: Chem.Biol.Drug Des. / Year: 2007 Title: Compensating enthalpic and entropic changes hinder binding affinity optimization. Authors: Lafont, V. / Armstrong, A.A. / Ohtaka, H. / Kiso, Y. / Mario Amzel, L. / Freire, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pk6.cif.gz | 62.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pk6.ent.gz | 45.1 KB | Display | PDB format |
PDBx/mmJSON format | 2pk6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/2pk6 ftp://data.pdbj.org/pub/pdb/validation_reports/pk/2pk6 | HTTPS FTP |
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-Related structure data
Related structure data | 2pk5C 1msmS 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: SUBTYPE B / Gene: gag-pol / Plasmid: pET24a+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03367, UniProt: Q9Q2G8*PLUS #2: Chemical | ChemComp-O33 / ( | #3: Chemical | ChemComp-GOL / | #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: 2.71 Å3/Da / Density % sol: 54.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 MES pH 6.5, 500 mM NaCl, 10 mM DTT, 3 mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 11, 2005 / Details: Osmic Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→33.54 Å / Num. obs: 41430 / % possible obs: 97.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Χ2: 1.932 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 1.73 / Num. unique all: 4071 / Rsym value: 0.806 / Χ2: 1.526 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MSM Resolution: 1.45→33.54 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.643 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.527 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→33.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.448→1.485 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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