[English] 日本語
Yorodumi- PDB-3vf5: Crystal Structure of HIV-1 Protease Mutant I47V with novel P1'-Li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vf5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of HIV-1 Protease Mutant I47V 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3vf5.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3vf5.ent.gz | 85.6 KB | Display | PDB format |
PDBx/mmJSON format | 3vf5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vf5_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3vf5_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3vf5_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 3vf5_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/3vf5 ftp://data.pdbj.org/pub/pdb/validation_reports/vf/3vf5 | HTTPS FTP |
-Related structure data
Related structure data | 3vf7C 3vfaC 3vfbC 3h5bS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10726.649 Da / Num. of mol.: 2 / Fragment: UNP residues 501-599 / Mutation: Q507K, L533I, I547V, L563I, C567A, C595A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 (BRU ISOLATE) Gene: gag-pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) / References: UniProt: P03367, HIV-1 retropepsin |
---|
-Non-polymers , 6 types, 215 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | ChemComp-031 / ( | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 54.31 % |
---|---|
Crystal grow | Temperature: 298 K / pH: 4.2 Details: NaCl/sodium acetate buffer at pH 4.2 The concentration of protein is around 1.5-1.6 mg/ml The ratio for protein/inhibitor is 1:5., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 18, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→10 Å / Num. obs: 61338 / % possible obs: 94.6 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.25→1.29 Å / Redundancy: 2 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 2.4 / % possible all: 63.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H5B Resolution: 1.25→10 Å / Num. parameters: 17853 / Num. restraintsaints: 24772 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 30 / Occupancy sum hydrogen: 1635 / Occupancy sum non hydrogen: 1717.75 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|