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Yorodumi- PDB-4ye3: Crystal Structure of Multidrug Resistant HIV-1 Protease Clinical ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ye3 | |||||||||
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Title | Crystal Structure of Multidrug Resistant HIV-1 Protease Clinical Isolate PR20 with Inhibitor GRL-4410A | |||||||||
Components | Protease | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HIV-1 Protease / Drug resistance / 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 group M subtype B | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | |||||||||
Authors | Agniswamy, J. / Weber, I.T. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Med.Chem. / Year: 2015 Title: Substituted Bis-THF Protease Inhibitors with Improved Potency against Highly Resistant Mature HIV-1 Protease PR20. Authors: Agniswamy, J. / Louis, J.M. / Shen, C.H. / Yashchuk, S. / Ghosh, A.K. / Weber, I.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ye3.cif.gz | 121.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ye3.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ye3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ye3_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4ye3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4ye3_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 4ye3_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/4ye3 ftp://data.pdbj.org/pub/pdb/validation_reports/ye/4ye3 | HTTPS FTP |
-Related structure data
Related structure data | 4yhqC 3ucbS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10766.542 Da / Num. of mol.: 2 Mutation: Q7K,L10F,I13V,I15V,D30N,V32I,L33F,E35D,M36I,S37N,I47V,I54L,Q58E,I62V,L63P,C67A,C95A,A71V,I84V,N88D,L89T,L90M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B Strain: isolate PR20 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, HIV-1 retropepsin |
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-Non-polymers , 5 types, 188 molecules
#2: Chemical | ChemComp-Y1 / #3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | ChemComp-G04 / ( | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.2M Sodium Chloride, 0.1M Sodium Acetate pH 5.5, 0.01M Yittrium Chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 21, 2013 |
Radiation | Monochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. obs: 38558 / % possible obs: 99.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.35→1.4 Å / % possible obs: 92.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UCB Resolution: 1.35→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.147 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.066 / 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: 19.96 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→50 Å
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