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Yorodumi- PDB-3kdb: Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I) in Complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kdb | ||||||
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Title | Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I) in Complex with KNI-10006 | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / VIRAL PROTEIN / Hydrolase / Protease / 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 / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...HIV-1 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 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Chufan, E.E. / Lafont, V. / Freire, E. / Amzel, L.M. | ||||||
Citation | Journal: Chem.Biol.Drug Des. / Year: 2010 Title: How much binding affinity can be gained by filling a cavity? Authors: Kawasaki, Y. / Chufan, E.E. / Lafont, V. / Hidaka, K. / 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 | 3kdb.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kdb.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 3kdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kdb_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3kdb_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3kdb_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 3kdb_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/3kdb ftp://data.pdbj.org/pub/pdb/validation_reports/kd/3kdb | HTTPS FTP |
-Related structure data
Related structure data | 3kdcC 3kddC 1msmS 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: 10804.808 Da / Num. of mol.: 2 / Fragment: UNP residues 501-599 / Mutation: Q7K, L33I, L63I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: SUBTYPE B / Gene: gag-pol / Plasmid: pET24a+ / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: P03367, HIV-1 retropepsin #2: Chemical | ChemComp-GOL / | #3: Chemical | ChemComp-006 / ( | #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: 2.72 Å3/Da / Density % sol: 54.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: citrate buffer pH 6.2, NaCl 500 mM, 100 mM DTT, 3mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: Apr 14, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→48.45 Å / Num. obs: 24519 / % possible obs: 85.9 % / Redundancy: 5.1 % / Rsym value: 0.06 / Net I/σ(I): 45.6 |
Reflection shell | Resolution: 1.66→1.72 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 2793 / Rsym value: 0.46 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MSM Resolution: 1.66→48.45 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.077 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.131 / 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: 25.863 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→48.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.661→1.704 Å / Total num. of bins used: 20
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