+Open data
-Basic information
Entry | Database: PDB / ID: 8esx | ||||||
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Title | HIV protease in complex with benzoxaborolone analog of darunavir | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE/INHIBITOR / virus / protease / inhibitor / boron / HYDROLASE / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Windsor, I.W. / Graham, B.J. / Raines, R.T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2023 Title: Inhibition of HIV-1 Protease by a Boronic Acid with High Oxidative Stability. Authors: Graham, B.J. / Windsor, I.W. / Raines, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8esx.cif.gz | 73.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8esx.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 8esx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8esx_validation.pdf.gz | 837.6 KB | Display | wwPDB validaton report |
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Full document | 8esx_full_validation.pdf.gz | 841.9 KB | Display | |
Data in XML | 8esx_validation.xml.gz | 13 KB | Display | |
Data in CIF | 8esx_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/8esx ftp://data.pdbj.org/pub/pdb/validation_reports/es/8esx | HTTPS FTP |
-Related structure data
Related structure data | 8esyC 6c8xS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10740.677 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I, C67A, C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: Q5RZ08 |
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-Non-polymers , 6 types, 220 molecules
#2: Chemical | ChemComp-GOL / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-ACT / | #6: Chemical | ChemComp-X7B / [( | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 54.02 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris pH 7.5 and 500 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.96862 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→48.1 Å / Num. obs: 50793 / % possible obs: 98.8 % / Redundancy: 11.8 % / Biso Wilson estimate: 17.61 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.076 / Net I/σ(I): 18.23 |
Reflection shell | Resolution: 1.35→1.39 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 3576 / CC1/2: 0.473 / Rrim(I) all: 2.263 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6c8x Resolution: 1.35→48.1 Å / SU ML: 0.1708 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6301 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→48.1 Å
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Refine LS restraints |
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LS refinement shell |
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