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Yorodumi- PDB-3vfa: Crystal Structure of HIV-1 Protease Mutant V82A with novel P1'-Li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vfa | ||||||
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Title | Crystal Structure of HIV-1 Protease Mutant V82A with novel P1'-Ligands GRL-02031 | ||||||
Components | protease | ||||||
Keywords | hydrolase/hydrolase inhibitor / protease inhibitor / P1'-ligand / 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 / 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 | Human immunodeficiency virus type 1 lw12.3 isolate | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | ||||||
Authors | Yu, X.X. / Wang, Y.F. / Chang, Y.C.E. / Weber, I.T. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Potent antiviral HIV-1 protease inhibitor GRL-02031 adapts to the structures of drug resistant mutants with its P1'-pyrrolidinone ring. Authors: Chang, Y.C. / Yu, X. / Zhang, Y. / Tie, Y. / Wang, Y.F. / Yashchuk, S. / Ghosh, A.K. / Harrison, R.W. / 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 | 3vfa.cif.gz | 103.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vfa.ent.gz | 78.8 KB | Display | PDB format |
PDBx/mmJSON format | 3vfa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vfa_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3vfa_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3vfa_validation.xml.gz | 12 KB | Display | |
Data in CIF | 3vfa_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/3vfa ftp://data.pdbj.org/pub/pdb/validation_reports/vf/3vfa | HTTPS FTP |
-Related structure data
Related structure data | 3vf5C 3vf7C 3vfbC 3h5bS 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: 10712.623 Da / Num. of mol.: 2 / Fragment: UNP residues 501-599 / Mutation: Q507K, L33I5, L563I, C567A, V582A, C595A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 lw12.3 isolate Gene: gag-pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) / References: UniProt: P0C6F2, HIV-1 retropepsin #2: Chemical | ChemComp-031 / ( | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CL / #5: 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: 2.31 Å3/Da / Density % sol: 54.25 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 0.6M NaCl, 0.1M Sodium Acetate buffer pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 / Wavelength: 1 Å | |||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 9, 2008 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.43→50 Å / Num. all: 39482 / Num. obs: 39482 / % possible obs: 90.5 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.1 | |||||||||
Reflection shell | Resolution: 1.43→1.48 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2 / Num. unique all: 2441 / % possible all: 57 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3H5B Resolution: 1.43→10 Å / Num. parameters: 16288 / Num. restraintsaints: 21882 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 16 / Occupancy sum hydrogen: 1631 / Occupancy sum non hydrogen: 1657.15 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→10 Å
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Refine LS restraints |
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