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Yorodumi- PDB-3ekq: Crystal structure of inhibitor saquinavir (SQV) in complex with m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ekq | ||||||
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Title | Crystal structure of inhibitor saquinavir (SQV) in complex with multi-drug resistant HIV-1 protease (L63P/V82T/I84V) (referred to as ACT in paper) | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / protease inhibitor / drug resistance / entropy enthalpy compensation / AIDS / Hydrolase-hydrolase inhibitor complex / Protease | ||||||
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 / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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 | HIV-1 M:B_ARV2/SF2 (virus) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Prabu-Jeyabalan, M. / King, N.M. / Schiffer, C.A. / Nalivaika, E. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2012 Title: Extreme Entropy-Enthalpy Compensation in a Drug-Resistant Variant of HIV-1 Protease. Authors: King, N.M. / Prabu-Jeyabalan, M. / Bandaranayake, R.M. / Nalam, M.N. / Nalivaika, E.A. / Ozen, A. / Yilmaz, N.K. / Schiffer, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ekq.cif.gz | 56.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ekq.ent.gz | 40.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ekq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ekq_validation.pdf.gz | 824 KB | Display | wwPDB validaton report |
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Full document | 3ekq_full_validation.pdf.gz | 825.5 KB | Display | |
Data in XML | 3ekq_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 3ekq_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/3ekq ftp://data.pdbj.org/pub/pdb/validation_reports/ek/3ekq | HTTPS FTP |
-Related structure data
Related structure data | 3ekpC 3ektC 3ekvC 3ekwC 3ekxC 3ekyC 3el0C 3el1C 3el4C 3el5C 3el9C 1f7aS 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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Details | One dimer (A & B identifiers) in one asymmetric unit |
-Components
#1: Protein | Mass: 10845.814 Da / Num. of mol.: 2 / Fragment: UNP residues 491-589 / Mutation: Q7K, L10I, G48V, I54V, V64I, V82T Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Strain: HXB2 / Gene: gag-pol / Plasmid: PXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106 / References: UniProt: P03369, HIV-1 retropepsin #2: Chemical | ChemComp-ROC / ( | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | THE INHIBITOR ROC IS A HYDROXYETH | |
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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: 2.15 Å3/Da / Density % sol: 42.69 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 28, 2008 / Details: Yale Mirrors |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→42 Å / Num. all: 12975 / Num. obs: 12975 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 6 |
-Processing
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Refinement | Starting model: PDB ENTRY 1F7A Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0 / SU B: 9.298 / SU ML: 0.182 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.334 / ESU R Free: 0.232 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.39 Å2 / Biso mean: 34.606 Å2 / Biso min: 17.31 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 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 |
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